The Whites temporarily went fourth on the table thanks to goals from former Latics striker Hugo Rodallega and veteran midfielder Damien Duff before Arouna Kone scored an injury-time consolation for the home side.
Rodallega was the man to open the scoring on his return to the DW Stadium when he rose above his marker just after the half-hour mark to fire home a header from Dimitar Berbatov's wonderful cross from the right for his first goal in Fulham colours since his summer move from Wigan.
Martin Jol's Fulham then doubled their advantage with just over 20 minutes remaining through Duff who received a clever pass from Bryan Ruiz, who was under pressure, with the Irishman slotting past Ali Al Habsi from around 16 yards.
Fulham were pretty much in control of proceedings from a scoreboard point of view but Wigan were looking dangerous with the lion's share of possession and more efforts on goal than their opponents.
They got their reward in the first minute of stoppage time when Kone fired home from six yards when substitute Callum McManaman's attempt from the edge of the box fell at his feet but it was not enough to deny the visiting Cottagers maximum points.
It would be a disappointing result for Roberto Martinez's Latics who looked the part at stages but defensive lapses cost them as they dropped to 15th with a second straight loss.
DW Stadium, Wigan - 19,284