Latics forced a late come back when Arouna Kone netted with minutes remaining but, Hugo Rodallega’s goal in the first half and Damien Duff right footed strike sealed a first away victory of the season for Fulham.
The home side dominated possession throughout but Fulham capitalised on their chances.
Roberto Martinez was made two changes going into the game with Ben Watson and Jordi Gomez coming in for James McArthur and Franco di Santo.
Latics started the game brightly and had carved out their first chance within 30 seconds when Kone blasted at Mark Schwarzer from distance but, the Australian comfortably gathered.
Fulham started to get the upper hand after 10 minutes but Latics defended well, clearing and stopping crosses from the wide areas.
Rodallega showed his dangerous side that Latics fans know all too well when he headed over on 19 minutes from a clipped Dimitar Berbatov cross, before Jean Beausejour was made to overhead kick a clearance when Chris Baird flicked on from Duff.
Just before the opening goal Latics had a perfect chance to take the lead themselves when Maynor Figueroa played a diagonal cross from the left to Emmerson Boyce at the back post but, the wide-man headed into the side netting.
Two minutes later and Rodallega made Latics pay from another clipped Berbatov cross, this time the Colombian rose high above the defence and thumped it past Ali Al Habsi.
With half time closing in and Latics still behind, Gomez nearly drew them level when his turn and shot inside the box from Beausejour’s cross rattled the cross bar.
After half time the theme of Latics’ dominance carried on and they had the ball in the net with three minutes played when Shaun Maloney placed in Gomez’s cut-back but the Spaniard had been judged offside from the original pass by James McCarthy.
Danger man Kone had a guilt edge chance to equalise on 57 minutes when McCarthy sliced open the defence from deep but with the Ivorian baring down on goal, out came Schwarzer to take advantage of the striker’s heavy touch and blocked the shot.
Ten minutes later and Fulham made it two against the run of play.
Substitute Bryna Ruiz held the ball up on the edge of the area and with Latics failing to clear he slipped in Duff down the right who lashed it past Al Habsi.
Martinez went all out to draw the scores level when he brought on Callum McManaman and Ryo Miyaichi with 13 minutes to go.
The Japanese winger started his appearance strongly and his cross from the right almost floated in at the back post but for Schwarzer to once again deny Latics.
McManaman was his tenacious self and showed just why he keeps on impressing in the Under 21s.
The goal late on came from his hard work as he took the ball down on his chest and hit a low volley into a crowd of players, the ball popped into Kone’s path and the striker lashed the ball into the bottom corner to make it 2-1.
Latics pushed hard with a minute and a half to play and even Al Habsi went forward when they won a late free kick but, the referee blew up for full time.
Latics: Al Habsi, Kone, McCarthy, Caldwell (c) (McManaman 77), Watson, Maloney, Gomez (Boselli 62), Boyce (Miyaichi 77), Ramis, Beausejour, Figueroa.
Subs: Pollitt, Jones, Crusat, McArthur
Fulham: Schwarzer, Riise, Hangeland (c), Baird, Sidwell, Berbatov, Duff, Hughes, Rodallega (Briggs 88), Reither, Kacaniklic (Ruiz 59)
Subs: Stockdale, Kelly, Kasami, Petric, Karagounis