Callum Lang’s 22nd-minute goal has given Wigan a 1-0 half-time lead over the Blues, who will feel they should have been awarded a penalty when Kyle Edwards was tripped inside the box.
Joe Pigott started alongside Macauley Bonne as interim manager John McGreal switched the Blues to a 4-4-2 system with Toto Nsiala, Sone Aluko and Scott Fraser dropping out of the XI.
Cameron Burgess took over from Nsiala at the heart of the defence with the back four otherwise the same as at Charlton on Tuesday. Ex-Latics loanee Christian Walton was in goal.
In midfield, former Wigan pair Sam Morsy and Lee Evans were in the centre with Conor Chaplin on the right with Kyle Edwards on the left.
Aluko and Fraser were on the bench, alongside James Norwood, who was back in the 18 for the first time since the Gillingham Papa John's Trophy tie game on October 5th.
Wigan Athletic included former Blues Will Keane and Gwion Edwards from the start.
After both teams and the official had taken a knee to applause from the two sets of supporters, the game got under way in steady rain with the Blues, wearing a black and grey away strip for the first time, taking the game to the home side in the opening couple of minutes.
But the Latics began to get on top and in the 10th minute James McClean crossed dangerously from the left and Janoi Donacien did well to get his head on the ball at the back post ahead of former Blue Edwards with Walton subsequently claiming.
Neither side threatened again until the 20th minute when Pigott was caught high by a boot as he held off a defender. The striker was off the pitch as Evans sent the free-kick to the far post but Bonne’s header looped well wide.
Within a minute, Wigan forced Walton into the first save of the game, Tom Pearce breaking away down the left before hitting a well-struck shot which the Blues’ keeper did well to palm over.
The resultant corner was forced behind from another flag-kick from which the Latics went in front. McClean sent the ball over, Walton saved from Gwion Edwards’s near-post flick-on but Lang was on hand to slam in from close range. Town complained at length that Lang had been offside but referee Trevor Kettle showed no interest, probably correctly.
The Blues had greater cause for frustration with the officials two minutes after the goal when Edwards beat two men, cut in from the left and then appeared to be tripped by Jack Whatmough. It looked a clear penalty and Town protested long and hard as referee Kettle awarded only a corner.
As the game passed the half-hour mark, the veteran official began to lose control. He first booked Conor Chaplin for an alleged trip on Pearce, although it appeared a clear dive, before seeming to reverse his decision to card the Blues’ forward after talking to his linesman.
Chaplin, who moments earlier had been held back after angrily pointing his finger at Pearce, quickly took a free-kick, presumably believing one had been awarded for the dive, before the referee stopped and indicated that it was still a Wigan free-kick.
Then, as things seemed to settle down, Pearce went down off the ball with Chaplin near him but with the Town players suggesting he had again taken a dive. Chaplin’s booking then appeared to be confirmed.
Order was restored but with one or two niggly challenges and Chaplin booed by the home support.
On 37, the Blues forced Ben Amos into his first save of the afternoon. Evans sent another free-kick from the left to the far post from where Bonne headed towards goal and the keeper dived to his left to claim two-handed with some comfort.
Blues interim boss McGreal approached referee Kettle at the whistle, presumably to get an explanation for the penalty decision and a number of other incidents after a puzzling and incoherent display from Mr Kettle.
Town hadn’t been too much better. After a reasonable first few minutes, they allowed Wigan to take control and then conceded from the first set piece.
The Blues’ only real threat from open play should have resulted in a penalty with Town’s only attempts Bonne’s headers from Evans’s free-kicks.
Chaplin may have been a touch still to be on after losing his head in the late incident, although to a great extent due to gamesmanship and poor officiating.
Wigan: Amos, Darikwa, Whatmough, Tilt, Pearce, Naylor, Power, Edwards, Keane, McClean, Lang. Subs: Janes, Kerr, Watts, Aasgaard, Massey, Jones, Humphrys.
Town: Walton, Vincent-Young, Edmundson, Burgess, Donacien, Morsy (c), Evans, Chaplin, Pigott, Edwards, Bonne. Subs: Hladky, Penney, Carroll, El Mizouni, Fraser, Aluko, Norwood. Referee: Trevor Kettle (Rutland).