The Championship hosts had the better of the first half and could easily have gone in at the break ahead, and were still in the game at 1-1 just after the hour mark.
However, they were only level for three minutes, and once Wigan had regained the lead in the 64th minute there was only ever going to be one winner.
Town started brightly and, within the first ten minutes, Chris Kirkland saved well from David Norris, before Ipswich had a penalty appeal rejected and Alan Quinn twice fired efforts off target.
Wigan's first attack almost brought a goal with Emile Heskey's bouncing volley being palmed away by Richard Wright.
Ipswich were extremely unlucky not to go ahead on 27 minutes when both Alex Bruce and Ivan Campo had efforts cleared off the line by Lee Cattermole and Titus Bramble respectively.
Tommy Miller curled a shot just wide for Town before Wright denied both Heskey and Cattermole, before the keeper made his best save when tipping Amr Zaki's free-kick onto the bar.
Wigan took the lead on 52 minutes when Wright could only parry Wilson Palacios's free-kick and it bounced in off a rather fortunate Cattermole.
Ipswich levelled nine minutes later when Jon Walters volleyed home Kevin Lisbie's cross, but Wigan regained the lead on 64 minutes when Olivier Kapo drilled home a loose ball from ten yards.
Ipswich came close to another equaliser when Campo's curled free-kick forced Kirkland into a fine tip over.
Almost immediately Wigan killed the game off with a third goal - Paul Scharner finishing from close range after Zaki had nodded down Antonio Valencia's corner.
The visitors put a somewhat unfair gloss on the scoreline in stoppage time when another Valencia corner was volleyed goalwards by Town old boy Bramble and substitute Henri Camara glanced a header beyond Wright.