Tommy Smith put the Blues in front but Wigan hit back via James McClean and Leon Barnett to lead 2-1 at the break.
Jonny Williams was handed his full Town debut with Sylvan Ebanks-Blake dropping to the bench in an otherwise unchanged side.
Williams started behind Daryl Murphy in a 4-4-1-1 formation, while former Blues loanee Ryan Tunnicliffe was in the Latics XI.
Smith blocked an early Martyn Waghorn shot after the on-loan Leicester man had cut in from the right but otherwise there was little action of note in either penalty area in the opening five minutes.
The Blues threatened for the first time in the sixth minute after Emmerson Boyce had fouled Stephen Hunt on the Town left. The Irishman whipped over the freekick and Paul Anderson sent a looping header onto the roof of Ali Al-Habsi’s net.
Jordi Gomez shot wide from distance for the Latics in the 15th minute, however, it had been the Blues doing most of the pressing, although without having created an opportunity. One or two debatable freekick decisions hadn’t endeared referee David Coote to the home crowd.
On 17 Paul Anderson, now on the left with Hunt on the right, crossed low and Murphy hit a shot on the turn which had Al-Habsi scrambling across to his left to paw the ball wide.
Two minutes later, the Blues went in front. Anderson was fouled just outside the area to the right and Hunt laid the ball to Cresswell, whose shot was blocked.
It ran to Cole Skuse, whose effort was also blocked but Wigan were unable to clear and the former Bristol City man eventually nodded the ball back into the danger area and Smith hooked home his fourth goal of the season from eight yards.
But the lead would last only three minutes. Boyce fed Marc-Antoine Fortune down the Wigan right and the former West Brom man cut the ball back to James McClean, who had pulled off his marker and slammed the ball past Dean Gerken from 10 yards.
Leon Barnett did well to head Williams’s cross out ahead of Murphy on 26 Town having broken quickly after a spell of Wigan possession in the Blues’ half.
Soon after McClean had been booked for a 37th minute foul on Williams, the Blues had a great chance to go back in front. Cresswell cut the ball across from the left, Anderson laid it back to Luke Hyam 10 yards out but the midfielder smashed the ball deep into the Sir Alf Ramsey Stand when he ought to at least have hit the target.
Three minutes before half-time, the visitors went ahead. Skuse fouled McClean on the Wigan left and Gomez curled the ball to the edge of the Town six-yard box from where Leon Barnett powered home a free header which Gerken couldn’t stop.
Neither side threatened to add to the goals in the remaining minutes with Town probably feeling they really oughtn’t to have been behind at the break.
Having gone in front, McClean was given far too much space in the penalty area for the first goal, while the Blues’ defending from the freekick which led to the second was even more questionable. Hyam will feel he should have put his team back in front just prior to Wigan’s second goal.
Ipswich: Gerken, Chambers (c), Berra, Smith, Cresswell, Skuse, Hyam, Anderson, Hunt, Williams, Murphy. Subs: Loach, Mings, Green, Tabb, Richardson, Taylor, Ebanks-Blake.
Wigan: Al Habsi, Boyce, Perch, Ramis, Barnett, McArthur, Tunnicliffe, Fortune, Waghorn. Subs: Carson, Crainey, Kiernan, McEachran, McManaman, Powell, McClean, Gomez, Maynard. Referee David Coote (Nottinghamshire).