Shaun Maloney scored the winner in the 50th minute at the DW Stadium, leaving United five points clear at the top after second-place Manchester City beat West Bromwich Albion 4-0.
"You wish the lead was better but considering where we were a few months ago, you have to take it," United manager Alex Ferguson said. "I said both teams would drop points."
The victory lifted a rejuvenated Wigan out of the relegation zone, with just five rounds remaining this season. It was the Latics first ever victory against United in 15 meetings.
United was flat and sloppy in possession, only coming to life in the final half-hour without really testing Wigan goalkeeper Ali Al Habsi. England striker Wayne Rooney was substituted in the 65th minute as United lost for the first time in the league since Jan. 4.
"We only had one shot on target and we were second to every ball," Ferguson said. "You have to recognize that Wigan are in a false position. They play some of the best football in the league, you have to credit them for that."
United could still have come away with an undeserved point had referee Phil Dowd spotted a handball by Wigan defender Maynor Figueroa in his own area, following a cross by Phil Jones late on.
Wigan, though, had a gripe of its own, when Victor Moses' headed goal from a 30th-minute corner was disallowed because Gary Caldwell was adjudged to have been impeding United goalkeeper David de Gea on the goalline.
"The most pleasing aspect is that the win was nothing lucky," Wigan manager Roberto Martinez said. "In our history, we've never taken a point from United and we restricted them to one shot on target.
"(But) it would be foolish to think we are out of the bottom three and we will stay there."
Maloney's only other goal this season came at Anfield on March 24, when Wigan beat Liverpool 2-1 to boost its attempts to avoid the drop. Since then, it has beaten Stoke and only lost at Chelsea on Saturday after conceding an injury-time goal and being on the end of contentious refereeing decisions, for which Martinez received an apology from officials this week.
Maloney's goal came after he exchanged passes with Jean Beausejour at a short corner. The diminutive Scotland forward cut inside, shimmied past Rooney and curled a shot that arched round De Gea into the corner.
Rooney curled just over with a long-range shot before being hauled off to be replaced by fit-again Portugal winger Nani.
United improved marginally but failed to find a cutting edge as it lost for only the fourth time in the league this season.