Philippe Senderos netted in the dying minutes as the hosts came from a goal down to condemn Wigan to their first defeat in two games.
The visitors headed into the match filled with confidence, having earned back-to-back wins after beating Manchester United and then Arsenal on Monday night.
And they took the lead just before the hour mark courtesy of an Emmerson Boyce strike, the defender’s fifth goal since joining the Latics in 2006.
However, Wigan’s lead was short-lived as January signing Pavel Pogrebyank drilled home just a minute later to level the score.
Moments later, the Russian international hit the crossbar before going onto strike the post – underlining the home side’s frustration at not being able to grab a goal.
And as it looked like the tie would end all square, former Arsenal centre back Philippe Senderos produced a bullet header in the 89th minute following John Arne Riise’s fierce free-kick.
Roberto Martinez’s men will feel hard done by leaving London with nothing, especially after their recent revival.
Fulham, meanwhile, move up to 49 points with this victory and now can look forward to Everton away next Saturday.
Man of the Match: Philippe Senderos
Referee: Lee Mason
Attendance: 25, 689
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