After a bright start from the home side, it was United who nearly found a way through on goal only for Gary Caldwell to block Javier Hernandez's shot.
The visitors threatened again soon after as Maynor Figueroa nearly put the ball into his own net from Ryan Giggs's effort.
Meanwhile, a determined Wigan tested David de Gea in the away goal when James McCarthy's 25-yard drive had to be turned over the top by the Spaniard.
The hosts had the ball in the net midway through the half, but Victor Moses's header from a corner was ruled out for Caldwell's soft foul on De Gea.
Despite protests from the home bench, there weren't any complaints five minutes into the second half as Shaun Maloney curled an exquisite shot past De Gea following a short corner routine with Moses.
United responded well to going behind and could have been awarded a penalty with 20 minutes to play after the ball looked to have struck Maynor Figueroa on the arm from Phil Jones's cross. However, referee Phil Dowd waved away the appeals.
As the away side pushed for an equaliser, Wigan nearly doubled their lead when De Gea had to pull off a good save from Moses's drive.
Moses threatened again in the final minutes when he dragged his shot wide of the post.
Michael Carrick had one last chance for United, but he could only put his weak shot over the bar.