Luke Hyam put the visitors ahead after 19 minutes and Conor Sammon's second-half strike sealed the points, despite Martyn Waghorn's late goal setting up a tense finish.
The result lifts Mick McCarthy's side up to seventh - just three points short of second spot - while Wigan, who qualified for the play-offs last season, are left languishing in 17th.
Hyam started and finished the move that broke the deadlock, the defender scoring his first goal of the season with a close-range finish from Tyrone Mings' cross.
Uwe Rosler's men were proving wayward with their finishing, a fact underlined by Andy Delort's off-target header from a threatening delivery.
Waghorn reduced the deficit when he helped James McClean's effort on its way into the net, and substitute Oriol Riera struck the post late on.
However, there was no way back for the hosts as Ipswich went some way to redressing the balance after losing twice to Wigan last term.
