Arouna Kone's last-minute goal gave Wigan a vital victory in a game marred by a horror tackle by Callum McManaman on Newcastle defender Massadio Haidara.
Jean Beausejour put the Latics in front when a McManaman cross was not cleared.
McManaman was not punished for a high lunge on Haidara and Magpies assistant John Carver was sent off after trying to confront the forward at half-time.
Pardew dismayed by "awful" tackle
Davide Santon levelled but Kone won it from a corner which Wigan defender Maynor Figueroa appeared to handle.
The win leaves Wigan three points adrift of safety, with a game in hand on fourth-bottom Aston Villa.
But Newcastle will feel aggrieved, firstly by how McManaman escaped a card for his dangerous challenge and also over Figueroa's handball to flick on the cross that led to Kone's scrambled winner.
Referee Mark Halsey did not even award a free-kick for McManaman's tackle on Haidara, who had been on the pitch for only a matter of minutes after replacing the injured Mathieu Debuchy.
The 20-year-old was eventually stretchered off after lengthy treatment.
Although McManaman did clip the ball, it was his follow through into Haidara's knee that did the damage. Newcastle's coaching staff reacted angrily and, along with Wigan first-team coach Graham Barrow, Carver saw red at half-time after scuffling as the teams headed for the tunnel.
Wigan's home woes
Despite their victory, the Latics have the joint-worst home record in England's top five divisions with three wins and 13 points from 15 games
Wigan had dominated the first half, with Newcastle's only meaningful early effort seeing Steven Taylor nod Sylvain Marveaux's corner straight at Latics keeper Joel Robles.
The Latics were well organised at the back and looking to break quickly down the flanks and it was from a cross that they took the lead on 18 minutes.
McManaman beat Haidara and lifted over a delivery that Santon could not clear, allowing Beausejour to pounce and drill home a low shot.
More Wigan chances followed, with Shaun Maloney seeing his curling shot saved and only a last-ditch challenge from Jonas Gutierrez denying James McCarthy after the midfielder burst clear.
And Newcastle remained on the backfoot immediately after the break, with only a smart block by Mapou Yanga-Mbiwa denying McManaman.
McManaman was taken off before the hour mark, bringing boos from the travelling Newcastle fans.
Martinez defends McManaman tackle
But it was a Magpies switch that appeared to have changed the game, with striker Shola Ameobi replacing midfielder Yoan Gouffran as Alan Pardew moved to a three-man defence that allowed Santon to venture further forward down the right.
The Italy defender did precisely that to level with 18 minutes remaining, latching on to Papiss Cisse's clever pass inside the Latics box after Wigan lost possession and burying a low shot into the bottom corner.
Cisse, who has scored two late winners in the past week, almost struck again from Ameobi's cross but Robles diverted his shot wide.
Instead it was Kone who settled an eventful match. Figueroa used his hand as he leapt to help on McCarthy's corner at the near post and, after the ball bounced around the Newcastle box and James Perch and Santon failed to deal with the danger, the Ivorian was in the right place to slam home from close range.
Wigan manager Roberto Martinez:
"Three points at this stage of the season is huge. We went through a period where we have to score a second goal otherwise it becomes difficult. But I could not be prouder of the character - especially at this stage of the season.
"Without scoring the second goal when we were leading 1-0, we found a way to win.
"The character was magnificent. They were very strong with good individual players who are a real threat.
"I don't feel we have had any luck whatsoever this season and the way we work I think we deserved that luck.
"We had so many opportunities and we couldn't find the final pass so we made it difficult, but we found a way to win and that pleased me."
Full Time The referee signals the end of the game.
Arouna Kone takes a shot. Davide Santon gets a block in. Short corner taken by Jordi Gomez from the right by-line.
Shola Ameobi takes a shot. Papiss Cisse is caught offside. Joel Robles takes the indirect free kick. Save made by Joel Robles.
Assist by Franco Di Santo.
89:51 Goal scored
Goal! - Arouna Kone - Wigan 2 - 1 Newcastle Arouna Kone finds the back of the net with a goal from close in high into the middle of the goal. Wigan 2-1 Newcastle.
A cross is delivered by James McCarthy, Cheick Tiote manages to make a clearance. Corner taken by Jordi Gomez from the right by-line,
Arouna Kone takes a shot. Cheick Tiote gets a block in.
Jonas Gutierrez delivers the ball, clearance made by Antolin Alcaraz.
Centre by Shola Ameobi, Shot from inside the six-yard box by Papiss Cisse goes wide right of the target.
Shola Ameobi challenges Paul Scharner unfairly and gives away a free kick. Antolin Alcaraz takes the free kick.
Foul by Franco Di Santo on Cheick Tiote, free kick awarded. Free kick taken by Rob Elliot.
Shaun Maloney fires a strike on goal direct from the free kick, save by Rob Elliot.
Substitution (Wigan) makes a substitution, with Franco Di Santo coming on for Jean Beausejour.
Foul by James Perch on Jean Beausejour, free kick awarded.
Davide Santon produces a cross.
Mapou Yanga-Mbiwa challenges Jordi Gomez unfairly and gives away a free kick. James McCarthy takes the direct free kick.
Free kick awarded for an unfair challenge on Davide Santon by Jordi Gomez. Rob Elliot takes the direct free kick.
The official flags Papiss Cisse offside. Joel Robles takes the free kick.
The assist for the goal came from Papiss Cisse.
71:05 Goal scored
Goal! - Davide Santon - Wigan 1 - 1 Newcastle Davide Santon scores a goal from inside the penalty area to the bottom left corner of the goal. Wigan 1-1 Newcastle.
Free kick awarded for a foul by Cheick Tiote on Jordi Gomez. Jordi Gomez restarts play with the free kick.
James McArthur takes a shot. Steven Taylor gets a block in. Inswinging corner taken left-footed by Jordi Gomez from the right by-line.
Corner from the left by-line taken by Jean Beausejour, Close range header by Maynor Figueroa goes over the crossbar.
Paul Scharner takes the direct free kick.
Substitution Shola Ameobi joins the action as a substitute, replacing Yoan Gouffran.
Booking Jonas Gutierrez booked.
Free kick awarded for a foul by Jonas Gutierrez on Shaun Maloney.
The assistant referee signals for offside against Moussa Sissoko. Free kick taken by Joel Robles.
A cross is delivered by Emmerson Boyce, save by Rob Elliot.
Free kick awarded for an unfair challenge on Shaun Maloney by Cheick Tiote. Free kick taken by Shaun Maloney.
James McArthur takes a shot. Davide Santon gets a block in. Jean Beausejour takes a outswinging corner.
Free kick awarded for an unfair challenge on Yoan Gouffran by James McArthur. Free kick taken by Sylvain Marveaux.
Substitution James McArthur replaces Callum McManaman.
Arouna Kone has an effort at goal from outside the penalty area which goes wide right of the goal.
Centre by Jean Beausejour, comfortable save by Rob Elliot.
Effort on goal by Papiss Cisse from just inside the penalty area goes over the target.
Unfair challenge on Sylvain Marveaux by Shaun Maloney results in a free kick. Sylvain Marveaux takes the free kick.
Shot from inside the area by Papiss Cisse clears the bar.
Callum McManaman takes a shot. Steven Taylor gets a block in.
Booking James Perch is cautioned.
The ball is sent over by Papiss Cisse. Moussa Sissoko has an effort at goal from just inside the box that misses to the left of the goal.
Outswinging corner taken from the left by-line by Sylvain Marveaux, save made by Joel Robles.
The second half begins.
45:00 +6:06 Half time
Half Time The ref blows to end the first period.
The ball is delivered by Davide Santon, clearance made by Emmerson Boyce.
Papiss Cisse takes a shot from inside the six-yard box clearing the crossbar.
Sylvain Marveaux produces a cross, clearance by Emmerson Boyce.
Free kick taken by Rob Elliot.
45:00 +2:47 Booking
Booking Paul Scharner shown a yellow card.
Paul Scharner gives away a free kick for an unfair challenge on Moussa Sissoko.
The ball is delivered by Jonas Gutierrez, Maynor Figueroa manages to make a clearance.
Arouna Kone gives away a free kick for an unfair challenge on Steven Taylor. Cheick Tiote restarts play with the free kick.
Corner from left by-line taken by Sylvain Marveaux.
A cross is delivered by Jean Beausejour.
James McCarthy takes a shot. Jonas Gutierrez gets a block in. Outswinging corner taken from the left by-line by Jean Beausejour, clearance made by Papiss Cisse.
Davide Santon gives away a free kick for an unfair challenge on Arouna Kone. Free kick taken by Jordi Gomez.
Shaun Maloney takes a shot. Rob Elliot makes a save.
Yoan Gouffran crosses the ball, save by Joel Robles.
Davide Santon gives away a free kick for an unfair challenge on Jean Beausejour. Maynor Figueroa takes the free kick.
The referee blows for offside against Papiss Cisse. Emmerson Boyce restarts play with the free kick.
Outswinging corner taken by Jean Beausejour.
Yoan Gouffran takes a shot. Callum McManaman gets a block in. Free kick awarded for a foul by Yoan Gouffran on Callum McManaman. Antolin Alcaraz restarts play with the free kick.
Callum McManaman is penalised for handball and concedes a free kick. The free kick is swung in left-footed by Sylvain Marveaux, Emmerson Boyce makes a clearance. Steven Taylor challenges Paul Scharner unfairly and gives away a free kick. Joel Robles restarts play with the free kick.
Substitution James Perch comes on in place of Massadio Haidara.
The offside flag is raised against Papiss Cisse. Shaun Maloney takes the free kick.
Cheick Tiote challenges Shaun Maloney unfairly and gives away a free kick. The free kick is swung in left-footed by Jordi Gomez.
Callum McManaman provided the assist for the goal.
17:16 Goal scored
Goal! - Jean Beausejour - Wigan 1 - 0 Newcastle Jean Beausejour grabs a goal from close range low into the middle of the goal. Wigan 1-0 Newcastle.
A cross is delivered by Callum McManaman,
The ball is crossed by Jean Beausejour, Davide Santon gets a block in. The ball is crossed by Maynor Figueroa, clearance made by Mapou Yanga-Mbiwa.
The referee blows for offside. Rob Elliot takes the free kick.
Substitution (Newcastle) makes a substitution, with Massadio Haidara coming on for Mathieu Debuchy.
The referee blows for offside. Joel Robles takes the indirect free kick.
Corner taken left-footed by Sylvain Marveaux from the right by-line, Steven Taylor takes a shot. Save by Joel Robles.
Arouna Kone fouled by Mapou Yanga-Mbiwa, the ref awards a free kick. Jordi Gomez has an effort direct from the free kick.
Centre by Emmerson Boyce, save made by Rob Elliot.
Moussa Sissoko sends in a cross, Antolin Alcaraz manages to make a clearance.
Jonas Gutierrez fouled by James McCarthy, the ref awards a free kick. Free kick taken by Jonas Gutierrez.
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