Kevin Keegan's expensively assembled side could make no headway before the interval and they fell behind six minutes into the second half when the former Manchester United defender Pat McGibbon headed home from a corner by Michael O'Neill.
David Lowe, Wigan's 33-year-old striker, who began his long career at Springfield Park more than 16 years ago, added the second after 62 minutes, again set up by O'Neill.
Three minutes later, Fulham had a golden opportunity to put themselves back in contention but their midfielder, Steve Hayward, had his penalty saved by Roy Carroll.
Still, Fulham had the chance to earn something out of the game. Wigan were reduced to 10 men when Paul Rogers was shown the red card for a late tackle that led to Steve Finnan being taken off on a stretcher, but Fulham were unable to exploit the advantage in the remaining 17 minutes.
Kevin Nugent's 49th-minute penalty lifted Cardiff City to the top of the Third Division. It gave the Welshmen a 1-0 victory at Carlisle United, who continue to struggle and remain in the bottom four. The Carlisle defender Tony Hopper brought down Richard Carpenter and Nugent made no mistake from the spot for his sixth goal of the season.
Mansfield Town moved up five places to third as they won by the same score at home to Peterborough United. Their leading scorer, Lee Peacock, knocked in the decisive goal after 14 minutes.Reuse content