Philippe Senderos's 89th-minute winner gave Fulham a dramatic victory which ended Wigan's recent revival.
The Latics, who have climbed out of the bottom three in recent weeks, led through Emmerson Boyce's fierce drive.
But Fulham levelled moments later when Pavel Pogrebnyak fired into the bottom corner and the Russian hit the bar from John Arne Riise's cross soon after.
Pogrebnyak hit the post again before Senderos won it with his header from Riise's whipped free-kick.
Senderos ends goal drought
Philippe Senderos's winner for Fulham was his first in the Premier League since he scored for Arsenal against Blackburn on 11 February 2008.
It was the Swiss defender's first goal since joining Fulham in June 2010 and, until he struck, it appeared Wigan would leave Craven Cottage with a hard-earned point to go with their unlikely wins in the last month.
After four victories in their last five games, including famous triumphs over Liverpool, Manchester United and Arsenal, the Latics already had daylight between themselves and the relegation zone but they were to fall agonisingly short of what would have been another step towards beating the drop.
Wigan had started like a train against the Gunners on Monday, with two goals in the first 10 minutes, but they were far more patient and pragmatic on their return to the capital.
With the visitors content to sit back, it was left to Fulham to try to find an attacking spark but they only sporadically managed to find a way through to Ali Al Habsi's goal.
The Cottagers' best early chance was a clever Danny Murphy free-kick that caught the Wigan defence napping, but Damien Duff blasted wastefully over at the near post.
Duff also curled wide after exchanging passes with Mahamadou Diarra and bursting into the area, while Clint Dempsey fired a couple of dangerous balls across the face of goal.
Wigan created little before the break but that changed in an eventful second half which produced plenty of goalmouth action and no little controversy.
The game exploded into life with Boyce's firecracker finish after 57 minutes, with the Wigan defender surging on to a loose ball after trying to find Connor Sammon on the edge of the box, and slamming a fierce low shot into the bottom corner.
But Fulham were behind for just 71 seconds, with Pogrebnyak providing an instant response from 20 yards out after good work from Moussa Dembele.
Pogrebnyak came within an inch of adding a second five minutes later when he met Riise's low cross, and it was unclear whether the ball had crossed the line or not after it came down off the bar.
The Russian striker turned to celebrate after connecting with the ball before seeing it bounce down and away. Linesman Mike Mullarkey did not flag for a goal and Pogrebnyak's reaction suggested he thought that was the right decision, and that he could not believe he had missed.
Fulham continued to press and Pogrebnyak went close again minutes later, when he could only steer his follow-up on to the post after Al Habsi had pushed away Dempsey's angled drive.
With the home side completely dominant, Senderos almost found the net inadvertently when Duff's cross hit Gary Caldwell and hit him before flying into the side netting.
The Cottagers were not to be denied, however, and they snatched the points when Senderos stooped to meet Riise's delivery from the left, and direct his header past the Wigan keeper.
Martin Jol's side were already mathematically safe from the drop and, after taking 10 points from their last four games, they are now looking up rather than down the table, with this win taking them up to ninth.
Fulham boss Martin Jol on Pogrebnyak's shot that hit the bar:
"I asked Pav and he said 'no, it was not over the line'.
"I thought therefore it was not over the line but our video guy showed me it was.
"It was a goal. Maybe what Sky or BBC saw was different but what I saw from my TV man was it was behind the line."
And Jol on the result: "It could have turned out differently but that is hypothetical and I am glad we won in the end. They had zero corners, no chances and they scored out of nothing so it would have been harsh if we had lost."
Wigan manager Roberto Martinez:
"I am disappointed with the result, with the manner the game ended.
"We knew it was going to be a very difficult game because first we knew Fulham are enjoying a very good season and are in good form and they had a lot more time to prepare.
"Obviously we had three very challenging games in eight days and today was probably a game too many. You could see that in spells.
"We allowed Fulham to come back and their equaliser was a very good strike from the edge of the box but a draw would have probably been a fair result so the set play at the end is a fantastic reward for Fulham."
Live Text Commentary
Full Time The final whistle goes and the game is over.90:00 +3:24
Free kick awarded for an unfair challenge on Philippe Senderos by Conor Sammon. Mark Schwarzer restarts play with the free kick.90:00 +0:52
Maynor Figueroa delivers the ball.90:00 +0:01
Free kick awarded for an unfair challenge on Damien Duff by Shaun Maloney. Mahamadou Diarra takes the free kick.88:21
The assist for the goal came from John Arne Riise.88:21 Goal scored
Goal! - Philippe Senderos - Fulham 2 - 1 Wigan Philippe Senderos finds the net with a headed goal from inside the penalty box. Fulham 2-1 Wigan.87:55
Unfair challenge on Kerim Frei by Emmerson Boyce results in a free kick. The ball is delivered by John Arne Riise,86:44 Booking
Booking Kerim Frei is shown a yellow card for unsporting behaviour.86:35
The ball is crossed by Victor Moses, Aaron Hughes makes a clearance.83:57
The assistant referee flags for offside against Victor Moses. John Arne Riise takes the indirect free kick.82:57
Free kick awarded for a foul by Victor Moses on Mahamadou Diarra. Free kick taken by John Arne Riise.82:19
The ball is sent over by Damien Duff.80:24
Damien Duff crosses the ball in from the free kick, clearance made by Gary Caldwell.80:24 Substitution
Substitution Danny Murphy goes off and Kerim Frei comes on.80:24
Foul by Jean Beausejour on Aaron Hughes, free kick awarded.78:36
Brede Hangeland fouled by Conor Sammon, the ref awards a free kick. Free kick taken by Brede Hangeland.77:38
Pavel Pogrebnyak has an effort at goal from inside the penalty box hitting the post.77:25
Clint Dempsey takes a shot. Save made by Ali Al Habsi.76:14
Free kick awarded for a foul by Maynor Figueroa on Damien Duff. Aaron Hughes restarts play with the free kick.74:59 Substitution
Substitution Ben Watson is brought on as a substitute for James McCarthy.
Shaun Maloney delivers the ball, Brede Hangeland makes a clearance.71:59
Maynor Figueroa sends in a cross, clearance made by Clint Dempsey.70:59
Brede Hangeland challenges Conor Sammon unfairly and gives away a free kick. Direct free kick taken by Gary Caldwell.70:45
Clint Dempsey takes a shot. Maynor Figueroa gets a block in.67:21
Damien Duff crosses the ball. Pavel Pogrebnyak gives away a free kick for an unfair challenge on Antolin Alcaraz. Free kick taken by Ali Al Habsi.66:49
John Arne Riise takes a shot. Save by Ali Al Habsi.65:38
Unfair challenge on Moussa Dembele by Maynor Figueroa results in a free kick. Danny Murphy takes the free kick.64:00
John Arne Riise takes a shot from inside the box clearing the bar.63:08
Corner taken short by Damien Duff.62:52
The ball is swung over by John Arne Riise, Pavel Pogrebnyak takes a shot.61:53
Danny Murphy restarts play with the free kick.61:53 Booking
Booking Emmerson Boyce receives a caution.61:44
Emmerson Boyce gives away a free kick for an unfair challenge on Clint Dempsey.57:49
Assist by Clint Dempsey.57:49 Goal scored
Goal! - Pavel Pogrebnyak - Fulham 1 - 1 Wigan Pavel Pogrebnyak gets on the score sheet with a goal from just outside the penalty box to the bottom right corner of the goal. Fulham 1-1 Wigan.56:38
Assist on the goal came from Conor Sammon.56:38 Goal scored
Goal! - Emmerson Boyce - Fulham 0 - 1 Wigan Goal scored by Emmerson Boyce from just outside the penalty area to the bottom left corner of the goal. Fulham 0-1 Wigan.55:52
Pavel Pogrebnyak gives away a free kick for an unfair challenge on Maynor Figueroa. Free kick taken by Gary Caldwell.54:53
Free kick taken by Danny Murphy.54:53 Substitution
Substitution Jordi Gomez goes off and Shaun Maloney comes on.54:53
Free kick awarded for a foul by James McCarthy on Danny Murphy.53:48
Emmerson Boyce sends in a cross, Maynor Figueroa has an effort at goal from just inside the box that misses to the right of the target.52:21
Direct free kick taken by Danny Murphy.52:21 Booking
Booking Gary Caldwell booked.52:15
Free kick awarded for a foul by Gary Caldwell on Pavel Pogrebnyak.51:29
Victor Moses takes a shot. Save by Mark Schwarzer.50:07
Unfair challenge on Jean Beausejour by Aaron Hughes results in a free kick. The ball is delivered by Jean Beausejour, Close range effort by Jordi Gomez misses to the right of the goal.45:31
Unfair challenge on Clint Dempsey by Antolin Alcaraz results in a free kick. Danny Murphy takes the direct free kick.45:01
The referee starts the second half.45:00 +0:46 Half time
Half Time It is the end of the first-half.43:13
Jordi Gomez takes a shot. Save by Mark Schwarzer.42:54
John Arne Riise produces a cross, Maynor Figueroa makes a clearance.42:33
Mahamadou Diarra fouled by James McArthur, the ref awards a free kick. Aaron Hughes restarts play with the free kick.40:45
The ball is sent over by Damien Duff, Gary Caldwell manages to make a clearance.39:48
Foul by Moussa Dembele on James McCarthy, free kick awarded. James McCarthy restarts play with the free kick.38:22
A cross is delivered by John Arne Riise, blocked by Emmerson Boyce.37:34
John Arne Riise produces a cross, Gary Caldwell manages to make a clearance.35:40
Jordi Gomez has an effort at goal from outside the penalty area which goes wide right of the goal.34:35
Clint Dempsey takes a shot. Save by Ali Al Habsi.34:07
Foul by Antolin Alcaraz on Clint Dempsey, free kick awarded. Direct free kick taken by John Arne Riise.33:52
Damien Duff produces a left-footed shot from deep inside the penalty box which goes wide of the left-hand post.32:17
Direct free kick taken by Antolin Alcaraz.32:17 Substitution
Substitution Conor Sammon joins the action as a substitute, replacing Franco Di Santo.32:17
Danny Murphy concedes a free kick for a foul on Antolin Alcaraz.30:53
Free kick awarded for an unfair challenge on Victor Moses by Philippe Senderos. Gary Caldwell takes the free kick.30:25
Unfair challenge on Maynor Figueroa by Pavel Pogrebnyak results in a free kick. Direct free kick taken by Maynor Figueroa.29:09
The ball is delivered by Clint Dempsey.27:36
The ball is sent over by Damien Duff, Ali Al Habsi makes a save.26:05
Jean Beausejour sends in a cross, clearance by Philippe Senderos.25:44
Clint Dempsey produces a cross, save made by Ali Al Habsi.25:10
The ball is sent over by Pavel Pogrebnyak, blocked by Gary Caldwell. Outswinging corner taken left-footed by Damien Duff from the left by-line, Franco Di Santo manages to make a clearance.24:59
The ball is swung over by Franco Di Santo, save by Mark Schwarzer.24:38
Free kick awarded for an unfair challenge on Danny Murphy by Victor Moses. Danny Murphy restarts play with the free kick.24:03
Clint Dempsey takes a shot. Gary Caldwell gets a block in. Moussa Dembele takes a shot. James McCarthy gets a block in.20:54
A cross is delivered by Jordi Gomez, save by Mark Schwarzer.19:40
Free kick awarded for an unfair challenge on Jordi Gomez by Mahamadou Diarra. Shot comes in from Jordi Gomez from the free kick.19:10
Clint Dempsey is ruled offside. Gary Caldwell takes the free kick.18:06
Corner taken left-footed by Damien Duff from the right by-line, Brede Hangeland has a headed effort at goal from close range which goes wide left of the target.17:54
Pavel Pogrebnyak takes a shot. Blocked by Gary Caldwell.12:54
The offside flag is raised against Pavel Pogrebnyak. Gary Caldwell restarts play with the free kick.11:07
Victor Moses takes a shot. Save by Mark Schwarzer.10:40
Free kick awarded for an unfair challenge on Antolin Alcaraz by Clint Dempsey. Antolin Alcaraz takes the direct free kick.9:00
Foul by Emmerson Boyce on John Arne Riise, free kick awarded. Danny Murphy delivers the ball, Shot on goal by Damien Duff from inside the box goes harmlessly over the target.8:34
Centre by Damien Duff, clearance by Emmerson Boyce.8:13
Corner taken short by Damien Duff.8:07
Damien Duff produces a cross, Gary Caldwell makes a clearance.6:12
Jean Beausejour crosses the ball, Effort from deep inside the area by Jordi Gomez misses to the left of the goal.4:39
Centre by Pavel Pogrebnyak.2:23
Foul by Mahamadou Diarra on James McCarthy, free kick awarded. Free kick crossed left-footed by Jean Beausejour, clearance by Mahamadou Diarra.0:00
The game kicks-off.
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