Clint Dempsey and Moussa Dembele gave the Cottagers their first away win of the season and pushed the Latics to the bottom of the table after their seventh straight defeat.
The hosts dominated the game and created plenty of chances but were unable to hit the target, and when they did they were denied by Mark Schwarzer and the frame of the goal. The visitors opened the scoring just before half time thanks to Clint Dempsey, with the American latching onto a low cross from Bobby Zamora to tap home his third goal of the season. They sealed the win with three minutes remaining through Mousa Dembele's low strike.
Both managers kept faith in the sides that lost their last games. Wigan welcomed back James McCarthy and Franco Di Santo to their matchday squad in place of Hendry Thomas and Jordi Gomez, while Shaun Maloney had to wait for his first start for the Latics.
Martin Jol called Pajtim Kasami and Matthew Briggs onto his subs bench in place of Aaron Hughes – who picked up an injury in training on Thursday – and youngster Karim Frei.
The game started off very nervously with both sides clearly understanding how crucial the match was, and for the opening 15 minutes both midfields prodded and probed for an opening without much success.
David Jones had two good looks in a first half devoid of many chances, as David Jones had one effort saved by Schwarzer and a well-taken volley fly just past the post.
The chances signaled the home side's beginning to control possession and it was clearly growing in confidence as the game went on as an outrageous effort on an overhead kick from Higo Rodallega nearly opened the scoring. Schwarzer continued to keep things level with a save on Ben Watson's volley, an effort which paid off just before halftime.
Just before the break, Fulham had its first sight of goal – Danny Murphy released Bobby Zamora on the left and there was a suspicion of offside, but the striker continued into the area and rolled a low cross towards the center of the goal and Dempsey put the ball into the back of the net to give the visitors the lead at the break.
The second half began much as the first did with both sides looking to keep possession whenever they could, Fulham went close through Johnson but the first real chance fell to the Moses in 54th minute as his sensational volley from 25 yards beat Schwarzer but crashed against the crossbar. Bobby Zamora had a chance to double the visitors' lead just after the hour mark but fired over.
The hosts did not give up and managed to get into excellent positions but their final efforts were either blocked or lacking in enough power to test Schwarzer. Rodallega went the closest as the game continued, as a long range free kick from the Colombian was denied by the Fulham keeper once more.
Maynor Figueroa also went close with six minutes to play, as the Fulham defense backed off him and he unleashed a thunderbolt which seemed to heading towards the corner but the ball clipped the post and rebounded wide with Schwarzer well beaten.
With three minutes remaining Fulham secured all three points through Dembele. The Belgian raced unchallenged from inside the Wigan half, he evaded one defender before side footing a shot past Al Habsi and into the bottom corner of the net to seal the win for the Cottagers with his first goal of the season.