Hugo Viana's strike gave Braga a win which leaves Birmingham's Europa League fate out of their own hands.
Blues started well and had the chance to lead but Nikola Zigic's penalty was saved after Ewerton fouled Wade Elliot.
Braga defender Ewerton should have been sent off for a second booking but stayed on and Viana then saw his long-range shot go in off Curtis Davies.
Birmingham now need to beat Maribor in their last group game in December to have any chance of progressing.
Braga are through and will be joined in the last 32 by Club Brugge if the two sides play out a draw in their final fixture in Belgium.
Did you know?
Nikola Zigic has scored just twice for Birmingham since his goal in last season's Carling Cup final
But should Braga win and Birmingham triumph over Maribor, Chris Hughton's side will qualify as a result of their superior head-to-head record over Brugge.
The Belgian side looked set for an exit as they trailed Maribor 3-0 but pulled off a remarkable comeback to score four times in the final 16 minutes to win 4-3.
Birmingham face Championship trips to play-off rivals Cardiff and Hull next week but Hughton named a strong side in Portugal and was rewarded with a superb opening quarter against last season's Europa League finalists.
Blues attacked from the off and could have had a penalty in the first minute when Chris Burke's cross struck the hand of Elderson inside the area.
Referee Markus Strombergsson waved play on but did award a spot-kick 10 minutes later when Ewerton was caught in possession by Elliott and then clumsily hauled him down.
The defender was booked but Zigic wasted the chance when his tame effort was easily stopped by Quim's sprawling save.
Ewerton then should have been sent off minutes later when he slid in rashly to bring down Burke on the edge of the area but he was somehow spared a second yellow card.
Steven Caldwell then saw a header saved by Quim as Birmingham piled on the pressure but eventually the hosts wrestled back control of the game and, with captain Alan influential after moving from the right flank to the left, began to look dangerous.
This season's Europa League final will be held in Bucharest
Midfielder Mossoro looped a 25-yard effort wide and then slalomed through two tackles to break into the area, only to be denied by a fine covering challenge from Keith Fahey.
Birmingham started the second period well but fell behind to a cruel deflected strike from former Newcastle man Viana.
The midfielder collected a ball from the right 30 yards from goal and saw his hopeful low shot strike Davies to deflect past a wrong-footed Boaz Myhill and into the bottom corner.
Zigic headed over a David Murphy cross as Birmingham rallied but the hosts should have sealed the win in the last few minutes.
Lima was sent free by a long ball and after Myhill made a strong save, substitute Paulo Cesar blazed the rebound over the top.
Hughton will now turn his attention towards moving into the the top six in the Championship but Blues could yet extend their European exploits beyond Christmas with victory over Maribor on 15 December.
- 01 Quim
- 05 Ewerton Booked
- 20 Echiejile (Douglao - 68' )
- 08 Mossoro (Merida - 84' )
- 22 Djamal
- 25 Leandro Salino
- 26 Vinicius
- 45 Viana
- 10 Barbosa (Paulo Cesar - 68' )
- 18 Lima
- 30 Alan Booked
- 32 Berni
- 02 Rodrigo Galo
- 44 Douglao
- 17 Merida
- 48 Nuninho
- 09 Paulo Cesar
- 21 Nuno Gomes
- 01 Myhill
- 03 Murphy
- 04 Caldwell Booked
- 23 Spector
- 24 Davies
- 07 Burke Booked
- 08 N'daw
- 11 Beausejour (Redmond - 64' )
- 15 Elliott (King - 64' )
- 18 Fahey
- 19 Zigic (Wood - 76' )
- 13 Doyle
- 05 Pablo
- 14 Gomis
- 22 Redmond
- 09 King
- 17 Rooney
- 39 Wood
Live Text Commentary
Full Time The final whistle goes and the game is over.90:00 +3:44
Effort on goal by Fran Merida from a long way out goes over the bar.90:00 +2:24
Free kick taken by do Carmo Leandro Salino.90:00 +2:24 Booking
Booking Chris Burke is cautioned.90:00 +2:21
Unfair challenge on Rodrigo Lima by Chris Burke results in a free kick.90:00 +1:52
Foul by Nascimento Paulo Vinicius on Chris Wood, free kick awarded. Free kick crossed by David Murphy, save by Silva Quim.90:00 +0:41
The referee blows for offside. Boaz Myhill restarts play with the free kick.90:00 +0:25
A cross is delivered by Marlon King, save by Silva Quim.89:45
Nathan Redmond challenges do Carmo Leandro Salino unfairly and gives away a free kick. Do Carmo Leandro Salino restarts play with the free kick.89:29
A cross is delivered by do Carmo Leandro Salino.87:42
Rocha Paulo Cesar gives away a free kick for an unfair challenge on Jonathan Spector. Boaz Myhill restarts play with the free kick.87:05
Chris Burke takes the inswinging corner, do Carmo Leandro Salino manages to make a clearance.86:03
Boaz Myhill restarts play with the free kick.86:03 Booking
Booking Osorio Alan goes into the referee's book for unsporting behaviour.86:01
Osorio Alan is penalised for a handball.85:06
The ball is crossed by Nathan Redmond, Nascimento Paulo Vinicius manages to make a clearance.83:16 Substitution
Substitution Fran Merida on for Marcio Mossoro.82:56
Rodrigo Lima takes a shot. Save made by Boaz Myhill.81:26
David Murphy concedes a free kick for a foul on Osorio Alan. Free kick taken by Silva Quim.79:57
Rodrigo Lima produces a drilled left-footed shot from 12 yards. Save by Boaz Myhill. Rocha Paulo Cesar produces a left-footed shot from inside the area that goes over the bar.
Corner taken by Miguel Hugo Viana from the right by-line, clearance by Guirane N'Daw.75:09 Substitution
Substitution Chris Wood replaces Nikola Zigic.73:40
The ball is sent over by Nikola Zigic.72:47
David Murphy produces a cross, Nikola Zigic produces a header from inside the area that goes over the bar.71:43
Inswinging corner taken by Miguel Hugo Viana from the right by-line, save made by Boaz Myhill.71:36
Miguel Hugo Viana crosses the ball, blocked by Guirane N'Daw.70:57
Corner taken left-footed by Miguel Hugo Viana from the right by-line, clearance by Nikola Zigic.70:47
Miguel Hugo Viana takes a shot. Steven Caldwell gets a block in.69:26
Unfair challenge on Marlon King by Nascimento Paulo Vinicius results in a free kick. David Murphy delivers the ball from the free kick left-footed from own half, clearance made by Ferreira Douglao.69:20
The ball is crossed by Marlon King.67:27
Outswinging corner taken by Chris Burke from the right by-line, Bindi Djamal manages to make a clearance. Nathan Redmond takes a shot. Bindi Djamal gets a block in.67:27 Substitution
Substitution (Braga) makes a substitution, with Rocha Paulo Cesar coming on for Jorge Helder Barbosa.67:27 Substitution
Substitution Ferreira Douglao replaces Uwa Echiejile.66:16
Marlon King delivers the ball, blocked by do Carmo Leandro Salino.65:12
Osorio Alan crosses the ball, clearance made by David Murphy.64:56
Jorge Helder Barbosa crosses the ball.63:18
Indirect free kick taken by Silva Quim.63:18 Substitution
Substitution Wade Elliott goes off and Marlon King comes on.63:18 Substitution
Substitution (Birmingham) makes a substitution, with Nathan Redmond coming on for Jean Beausejour.63:18
The offside flag is raised against Nikola Zigic.62:30
Wade Elliott takes the outswinging corner, clearance made by Santos Ewerton. Steven Caldwell crosses the ball, save by Silva Quim.62:24
The ball is swung over by Chris Burke, Santos Ewerton gets a block in.61:00
Rodrigo Lima takes a shot. Save made by Boaz Myhill.59:22
David Murphy crosses the ball, clearance made by Nascimento Paulo Vinicius.57:59
Do Carmo Leandro Salino takes a shot. Blocked by Curtis Davies.57:27
Corner taken right-footed by Osorio Alan, save made by Boaz Myhill.56:57
Marcio Mossoro crosses the ball, Bindi Djamal takes a shot. Blocked by Steven Caldwell.56:13
Guirane N'Daw produces a right-footed shot from just outside the penalty area that goes harmlessly over the target.55:42
Outswinging corner taken by Wade Elliott from the right by-line, Nascimento Paulo Vinicius manages to make a clearance.55:29
Inswinging corner taken right-footed by Wade Elliott from the left by-line, Silva Quim makes a save.55:03
Corner from the left by-line taken by Wade Elliott, clearance by Osorio Alan.54:48
The ball is sent over by Chris Burke, clearance made by Nascimento Paulo Vinicius.54:24
Chris Burke delivers the ball, clearance made by Uwa Echiejile.53:53
Shot from outside the area by Jean Beausejour misses to the left of the target. Keith Fahey takes a shot. Miguel Hugo Viana gets a block in.52:13
Rodrigo Lima challenges Jonathan Spector unfairly and gives away a free kick. Free kick taken by Keith Fahey.50:32
The assist for the goal came from Osorio Alan.50:32 Goal scored
Goal! - Miguel Hugo Viana - Braga 1 - 0 Birmingham A goal is scored by Miguel Hugo Viana from just outside the box to the bottom left corner of the goal. Braga 1-0 Birmingham.49:50
The assistant referee flags for offside against Nikola Zigic. Indirect free kick taken by Silva Quim.48:48
Unfair challenge on do Carmo Leandro Salino by Guirane N'Daw results in a free kick. Do Carmo Leandro Salino restarts play with the free kick.46:56
Foul by Jorge Helder Barbosa on Jean Beausejour, free kick awarded. Boaz Myhill takes the free kick.45:43
The ball is sent over by David Murphy, clearance made by Nascimento Paulo Vinicius.45:01
The match restarts for the second half.45:00 +1:04 Half time
Half Time The ref blows to signal half-time.45:00 +0:13
The ball is crossed by Osorio Alan, clearance made by Steven Caldwell.43:57
Long range effort by Miguel Hugo Viana goes over the target.43:23
Keith Fahey takes a shot. Save made by Silva Quim.42:12
The ball is delivered by do Carmo Leandro Salino, clearance made by Chris Burke.40:43
The ball is delivered by Jonathan Spector, save by Silva Quim.39:26
The ball is crossed by Osorio Alan.38:54
Free kick taken by do Carmo Leandro Salino.38:54 Booking
Booking Steven Caldwell receives a caution for unsporting behaviour.38:38
Steven Caldwell concedes a free kick for a foul on Rodrigo Lima.37:18
Foul by David Murphy on do Carmo Leandro Salino, free kick awarded. Silva Quim takes the free kick.36:42
Free kick awarded for an unfair challenge on Wade Elliott by Jorge Helder Barbosa. Boaz Myhill takes the free kick.35:29
The referee gives a free kick against Marcio Mossoro for handball. Free kick taken by Steven Caldwell.33:34
The ball is swung over by Jorge Helder Barbosa.32:24
Rodrigo Lima takes a shot from a long way out which goes wide of the right-hand upright.32:04
Osorio Alan crosses the ball, clearance by Steven Caldwell.31:08
Do Carmo Leandro Salino delivers the ball, clearance by Jonathan Spector.30:51
Jorge Helder Barbosa produces a cross, clearance made by Curtis Davies.30:13
Nascimento Paulo Vinicius fouled by Wade Elliott, the ref awards a free kick. Santos Ewerton restarts play with the free kick.29:48
Shot from just outside the box by Jorge Helder Barbosa misses to the left of the target.29:07
Corner from the left by-line taken by Osorio Alan, clearance made by Jonathan Spector.27:27
Foul by Guirane N'Daw on Marcio Mossoro, free kick awarded. The free kick is swung in left-footed by Miguel Hugo Viana, clearance by Guirane N'Daw.26:47
Free kick awarded for a foul by do Carmo Leandro Salino on David Murphy. David Murphy restarts play with the free kick.25:48
Marcio Mossoro has an effort at goal from outside the penalty area which goes wide right of the goal.25:40
Miguel Hugo Viana sends in a cross, clearance by Jonathan Spector.24:51
Corner taken right-footed by Osorio Alan from the left by-line, save made by Boaz Myhill.24:36
The ball is crossed by do Carmo Leandro Salino, Curtis Davies manages to make a clearance.23:47
Jorge Helder Barbosa produces a cross, clearance made by David Murphy.22:45
The assistant referee signals for offside against Chris Burke. Free kick taken by Miguel Hugo Viana.21:21
Marcio Mossoro challenges Jean Beausejour unfairly and gives away a free kick. Direct free kick taken by David Murphy.21:08
The ball is crossed by Miguel Hugo Viana, clearance made by Curtis Davies.19:43
Unfair challenge on Osorio Alan by Jean Beausejour results in a free kick. Direct free kick taken by Bindi Djamal.19:27
The ball is sent over by Chris Burke, save by Silva Quim.18:45
The offside flag is raised against Marcio Mossoro. Boaz Myhill takes the free kick.18:30
The ball is swung over by Osorio Alan, Curtis Davies manages to make a clearance.17:30
Do Carmo Leandro Salino crosses the ball, Steven Caldwell manages to make a clearance.16:50
Marcio Mossoro produces a cross, blocked by Steven Caldwell.14:44
Inswinging corner taken right-footed by Wade Elliott, clearance made by Nascimento Paulo Vinicius.13:59
Jorge Helder Barbosa concedes a free kick for a foul on Keith Fahey. David Murphy delivers the ball, Jean Beausejour takes a shot. Save by Silva Quim.12:33
Santos Ewerton challenges Chris Burke unfairly and gives away a free kick. David Murphy has an effort direct from the free kick, save by Silva Quim.11:10
Outswinging corner taken by Wade Elliott from the right by-line, Osorio Alan makes a clearance.11:00 Penalty
Placed penalty taken by Nikola Zigic saved by Silva Quim. Braga 0-0 Birmingham.9:51 Booking
Booking Santos Ewerton is cautioned by the ref for unsporting behaviour.9:44
Wade Elliott fouled by Santos Ewerton, the ref awards a Penalty.8:50
Foul by Chris Burke on Uwa Echiejile, free kick awarded. Direct free kick taken by Uwa Echiejile.8:27
Curtis Davies fouled by Rodrigo Lima, the ref awards a free kick. Curtis Davies restarts play with the free kick.6:46
Unfair challenge on Jonathan Spector by Jorge Helder Barbosa results in a free kick. Direct free kick taken by Jonathan Spector.5:14
Chris Burke delivers the ball, Headed effort from deep inside the area by Jean Beausejour misses to the right of the goal.3:34
Osorio Alan takes a short corner. Osorio Alan produces a cross, blocked by Wade Elliott.3:21
Osorio Alan produces a cross, clearance by Jonathan Spector.2:38
Miguel Hugo Viana crosses the ball, clearance made by Curtis Davies.2:01
Curtis Davies concedes a free kick for a foul on Rodrigo Lima. Miguel Hugo Viana takes the free kick.1:18
Outswinging corner taken by Wade Elliott, Bindi Djamal makes a clearance.1:03
Chris Burke sends in a cross, blocked by Uwa Echiejile.0:00
The game kicks-off.
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