The Latics had a vital point stolen from their grasp after the Cottagers' defender netted in the last minute, after a largely dull game which looked destined to end as a draw
The first-half saw little action with the visitors happy to sit deep and allow the Cottagers to try and break them down, which they mostly failed.
However, two quick-fire goals in the second half from either side gave the match a glimmer of hope, then with the hosts increasing the pressure in the last 20 minutes they bagged a winner in the 90th minute.
The early pressure was all from the home side, Clint Dempsey and Pogrebnyak linked up well numerous times in the opening 10 minutes, however they were unable to create any clear-cut chances.
It was then Wigan which had the first chance of the game, Franco Di Santo tried his luck with a volley after Maynor Figueroa sent the ball in from the left, but the Latics man lashed his effort over.
The hosts then managed to get a slight foothold in the match, with the front two again showing some touches of class, and it was indeed Fulham which had the next clear chance.
John Arne Riise was brought down by Emerson Boyce on the left side, which presented Danny Murphy an opportunity to put the ball into the box from the free-kick. However, he tricked everyone in the ground by rolling it to Damien Duff but unfortunately for Jol's men, he miss-hit his shot and sliced the effort over.
After a slightly promising opening 20 minutes from the hosts, the fact that Martin Jol's side has nothing left to play for seemed to set in. The Cottagers were casual at times and lacked real penetration. Duff took a corner which was met with no challenge in the air and for long spells the ball was just hit from end to end.
As the half-hour mark approached the home side did carve out a good opening. John Arne Riise, who was up and down the left-flank all day, slotted it through to Dempsey who then rolled the ball along the face of goal. WIth Ali Al-Habsi stranded all it needed was a touch in but no-one was busting a gut to finish.
The Wigan faithful thought they had scored five minutes into the second half when Gomez scrambled an effort at goal, after the Latics' corner was headed on to him. However, the ball only managed to ripple the side netting.
The visitors broke the deadlock with 57 minutes played, Boyce beating Schwarzer with a long-range low effort. However just as the traveling crowd looked up Pogbrebnyak hit back with an instant equalizer.
The Cottagers then had a brilliant chance to take the lead and their fans must have been left wondering how they didn't. Riise hit a cross into the ground which bypassed Al-Habsi but Pogrebnyak somehow hit the bar from two yards out, although replays suggest the ball may have crossed the line. Minutes later Pogrebnyak again nearly gave the hosts the lead but his header went just over the bar.
With 20 minutes to play things died down once more and both sides were cautious. Then with nearly 10 minutes left Pogbrebnyak again somehow managed to fluff a glorious chance. Al-Habsi made a good initial save but as the ball fell but to the forward, he completely miss-hit the ball and was denied by the post.
Fulham continued to push for a winner in the final stages and was desperately unlucky when after a free-kick from the right hand side, a Wigan defender's clearance hit Philipe Senderos but just went inches wide.
However, the former Arsenal player did get a bit of a luck in the final minute when he got his head on a cross to nod home the winner. Senderos' goal condemns Wigan to a nail-biting final three games.