Fulham's form at Craven Cottage has been the key to their survival and this was their 13th home win in 21 games in all competitions.
But it was hardly a thriller as Malbranque's well-taken goal on the stroke of half-time was a rare highlight. And they could have thrown it away in the very last minute when David Connolly somehow missed from right in front of goal - and Henri Camara turned the loose ball into the sidenetting.
The result is a bitter blow to Wigan's hopes of qualifying for the UEFA Cup and they can only blame themselves after missing a series of chances.
In a first half that was bitty and uninspiring, both sides struggled to turn an end-of-season stroll into a more meaningful contest - until right at the end.
Fulham were wasteful in possession and sloppy in defence while Wigan failed to take advantage.
They did create a wonderful chance, however, when a slip from Ian Pearce after 10 minutes allowed Gary Teale a free shot on goal, but keeper Antii Niemi made a superb one-handed save to turn it away.
Fulham had one or two half-chances, Heidar Helguson heading straight at keeper Mike Pollitt from a Wayne Bridge cross and Malbranque seeing an early 25-yarder well saved.
But Wigan remained the more likely scorers with midfielders Teale and Jimmy Bullard at least trying to force the pace in between scrappy passages of play.
Lee McCulloch had a header saved from an excellent deep Bullard cross after 29 minutes and Jason Roberts nodded wide from a ball whipped in by Teale.
But there was little excitement for the Craven Cottage crowd to enjoy at the other end until Malbranque burst into life in injury time
Luis Boa Morte put him through on goal with a neat pass between two defenders and Malbranque's high left-foot finish was instant and impressive.
It wasn't enough to keep the home crowd happy, however - because one section of the Stevenage Road stand booed the side off despite the goal!
Fulham maintained their momentum after the break, with Helguson seeing an instant shot well saved in the very first minute. And then Brian McBride just failed to connect with a deflected Malbranque effort with an open goal gaping in front of him.
Wigan's best chance fell to Bullard, who saw his effort well saved by Niemi midway through the second half after being set up by Jason Roberts. And the game was at least more lively than earlier in the evening.
Boa Morte was lucky to stay on the field when he was booked for a late challenge on Teale and Roberts had a goal disallowed because Wigan took the free-kick to him too quickly.
There was no doubt that the visitors looked more hungry but Malbranque was the classiest player on show, stinging keeper Pollitt's hands with a 81st minute piledriver.
Fulham held on comfortably until the very last second, when Connolly mis-hit his shot and Camara couldn't squeeze the ball home as it ran loose.