Carlos Edwards scored late for Ipswich to keep them four points clear of relegation as Bolton's late-season play-off push took a blow.
The Ipswich midfielder missed an early chance when he headed wide from close range before Daryl Murphy shot off target for the hosts at Portman Road.
David Ngog missed Bolton's best chance when he headed wide from substitute Kevin Davies' cross after the break.
Bolton's away day blues
Bolton have lost just three league games in 2013 and all have come away from home. They have won just three Championship away games this season
With two minutes to go, Jay Emmanuel-Thomas crossed for Edwards to turn in.
Bolton came into the game with hopes of making the play-offs following an eight-match unbeaten run which included five wins in a row.
But they rarely threatened Ipswich in a disappointing first-half for Dougie Freedman's side with Edwards, Andy Drury and Murphy going close for Mick McCarthy's Tractor Boys.
After the break, Murphy lifted a shot over when David McGoldrick was in a better position before Chris Eagles scuffed a shot wide for Bolton.
Davies' introduction improved Bolton and Tommy Smith had to block the Trotters' club captain from scoring.
Ngog then squandered his chance before Emmanuel-Thomas charged down the wing and crossed for Edwards who secured the three points.
Ipswich manager Mick McCarthy:
"I've got friends in my office and just went in there and shouted, 'You beauty'.
"It was a huge result and a great three points. Teams don't come much more in-form than Bolton.
"To be fair, we've done alright against the form teams - we've struggled against the likes of Barnsley, Peterborough and Bristol City.
"I don't know why that should be, but we've certainly progressed. We've got better and become harder to beat.
"We had a really good first half.
"They had a spell in the second when they got on top, but when we changed our shape and stemmed the tide we deserved to win overall."
Bolton manager Dougie Freedman:
"Obviously we're disappointed with the result.
"It was a very hard-fought and physical Championship game. From the 60th minute onwards, I thought we were dominant in possession and created a few opportunities.
"We could have worked their goalkeeper a bit more, but we looked the more capable team towards the end and the most likely to score.
"We had the ball in the right areas, but were perhaps let down by the last decision whether to shoot, cross or control the ball in vital areas."
Live Text Commentary
Full Time The referee signals the end of the game.90:00 +2:38
David Ngog is caught offside. Free kick taken by Stephen Henderson.87:45 Substitution
Substitution Marvin Sordell replaces Craig Dawson.87:45
Jay Emmanuel-Thomas provided the assist for the goal.87:45 Goal scored
Goal! - Carlos Edwards - Ipswich 1 - 0 Bolton A goal is scored by Carlos Edwards from inside the area to the bottom left corner of the goal. Ipswich 1-0 Bolton.87:20
The ball is sent over by Jay Emmanuel-Thomas, Carlos Edwards takes a shot. Craig Dawson gets a block in.84:27
Free kick awarded for a foul by Darren Pratley on Aaron Cresswell. Direct free kick taken by Stephen Henderson.83:06
Carlos Edwards takes a shot. Comfortable save by Andy Lonergan.81:20
Free kick awarded for an unfair challenge on Jay Emmanuel-Thomas by Samuel Ricketts. Free kick taken by Andy Drury.80:15
David Ngog sends in a cross, clearance made by Tommy Smith.78:28
Foul by Jay Emmanuel-Thomas on Chung-Yong Lee, free kick awarded. Direct free kick taken by Jay Spearing.77:47 Substitution
Substitution Jay Tabb leaves the field to be replaced by Michael Chopra.75:13 Substitution
Substitution (Ipswich) makes a substitution, with Jay Emmanuel-Thomas coming on for David McGoldrick.74:52
Kevin Davies produces a cross, Header from close in by David Ngog misses to the right of the goal.70:39
The ball is sent over by Chris Eagles, Tommy Smith manages to make a clearance.69:19
Marcos Alonso produces a cross.68:37
A cross is delivered by Samuel Ricketts, Carlos Edwards manages to make a clearance.66:31
Chris Eagles delivers the ball, clearance made by Jay Tabb.65:40
Shot from long range by Andy Drury misses to the right of the goal.65:14 Substitution
Substitution Kevin Davies replaces Craig Davies.
The ball is crossed by David McGoldrick, clearance made by Zat Knight.62:09
Free kick taken by Stephen Henderson.62:09 Booking
Booking The referee books Craig Davies for unsporting behaviour.62:06
Craig Davies is penalised for handball and concedes a free kick.60:57
David McGoldrick sends in a cross.59:36
Outswinging corner taken by Jay Spearing from the right by-line, Foul by Zat Knight on Luke Chambers, free kick awarded. Free kick taken by Stephen Henderson.58:34
Shot from deep inside the area by Chris Eagles clears the bar.57:42
The referee blows for offside. Andy Lonergan takes the indirect free kick.56:21
Outswinging corner taken right-footed by Jay Spearing from the right by-line, save made by Stephen Henderson.55:53
Corner taken right-footed by Jay Spearing, clearance made by Daryl Murphy.55:17
Free kick awarded for an unfair challenge on Jay Spearing by Jay Tabb. Samuel Ricketts takes the free kick.52:28
Samuel Ricketts sends in a cross, Aaron Cresswell gets a block in.50:43
Craig Davies takes a shot from long range which goes wide of the right-hand post.49:59
Effort on goal by Daryl Murphy from deep inside the area goes harmlessly over the bar.46:57
Corner taken by Jay Spearing from the left by-line, save by Stephen Henderson.46:48
Centre by Marcos Alonso, save made by Stephen Henderson.45:56
The ball is crossed by Chung-Yong Lee, Daryl Murphy manages to make a clearance. Corner from the right by-line taken by Jay Spearing, clearance by Richard Stearman.45:03
Effort on goal by Craig Davies from just inside the box goes harmlessly over the target.45:01
The second half begins.45:00 +1:17 Half time
Half Time The referee calls an end to the first half.45:00 +0:42
Free kick awarded for a foul by Marcos Alonso on Carlos Edwards. Free kick taken by Stephen Henderson.41:03
Carlos Edwards sends in a cross, Chung-Yong Lee manages to make a clearance.39:09
Centre by Marcos Alonso, clearance made by Aaron Cresswell.37:46
Corner taken by Aaron Cresswell, David Ngog makes a clearance.37:09
The ball is delivered by Daryl Murphy, clearance made by Jay Spearing.35:07
Long range shot from Marcos Alonso misses to the left of the target.33:59
Craig Davies takes a shot. Stephen Henderson makes a save.29:58 Booking
Booking Darren Pratley goes into the book.29:23
Centre by Jay Tabb, clearance made by Chris Eagles.28:58
The ball is crossed by David Ngog, clearance made by Luke Chambers.26:13
David McGoldrick produces a cross, Craig Dawson manages to make a clearance.25:28
A cross is delivered by Aaron Cresswell, clearance by Darren Pratley.23:52
Craig Davies is flagged offside by the assistant referee. Stephen Henderson restarts play with the free kick.23:12
Outswinging corner taken by Jay Spearing from the right by-line, clearance by Aaron Cresswell.21:40
The ball is delivered by David McGoldrick, Effort from inside the six-yard box by Daryl Murphy goes wide left of the target.20:56
The referee blows for offside. Stephen Henderson takes the free kick.18:43
Outswinging corner taken from the right by-line by Jay Spearing, Richard Stearman manages to make a clearance.17:14
Effort from inside the area by David McGoldrick misses to the right of the target.16:29
Marcos Alonso takes a shot. Blocked by Richard Stearman. Effort on goal by Chris Eagles from outside the penalty box goes harmlessly over the bar.14:30
David McGoldrick delivers the ball, Andy Drury takes a shot. Save made by Andy Lonergan.12:26
Andy Drury sends in a cross, Close range headed effort by Carlos Edwards misses to the right of the goal.12:00
Aaron Cresswell produces a cross, Samuel Ricketts gets a block in.11:35
Centre by Aaron Cresswell, Marcos Alonso manages to make a clearance.10:49
The ball is crossed by Andy Drury, clearance by Craig Dawson.10:13
Aaron Cresswell concedes a free kick for a foul on Marcos Alonso. Jay Spearing restarts play with the free kick.5:48
Carlos Edwards delivers the ball, clearance made by Zat Knight.5:05
Free kick awarded for an unfair challenge on Jay Tabb by Samuel Ricketts. Free kick taken by Aaron Cresswell.4:41
A cross is delivered by Chris Eagles, clearance by Luke Chambers.3:25
The ball is delivered by Luke Hyam, Zat Knight manages to make a clearance.2:45
Free kick awarded for a foul by Craig Davies on Richard Stearman. Direct free kick taken by Stephen Henderson.2:33
Samuel Ricketts produces a cross, Richard Stearman makes a clearance.1:25
Unfair challenge on Chung-Yong Lee by Andy Drury results in a free kick. Direct free kick taken by Jay Spearing.0:45
David McGoldrick takes a shot. Save by Andy Lonergan.0:00
The referee gets the game underway.
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