Brett Pitman put the Blues ahead from the penalty spot in the seventh minute but Yanic Wildschut equalised for Wigan on 35 to leave the scores level at half-time.
Pitman, Andre Dozzell, Jonny Williams, Freddie Sears and Jonas Knudsen all started for the Blues as Mick McCarthy made five changes from the team which lost 2-1 at Birmingham on Tuesday.
Knudsen returned to his usual left-back role having recovered from the hamstring injury, which saw him miss the game at St Andrew’s.
Dozzell, making his first Championship start of the season, and Williams, making his first start of his fourth spell at the club, lined-up ahead of Cole Skuse in a central midfield three.
Up front, Pitman started as the central striker with Tom Lawrence on the left and Freddie Sears on the right.
Myles Kenlock, David McGoldrick, Grant Ward, Luke Varney and Jonathan Douglas all dropped to the bench.
Wigan made three changes with the injured Craig Morgan, Shaun MacDonald and Luke Garbutt dropping out and Dan Burn, Jordi Gomez and Andy Kellett coming into the team.
The Blues, in their Barcelona-esque third kit, had the better of the opening few minutes of a game which started in fog, although not thick enough to impact on players or watching supporters.
The match stopped in the fourth minute when Pitman and Burn clashed heads and required treatment before continuing.
Town continued to dominate the early stages and in the seventh minute were awarded a penalty.
Lawrence, who played for Wigan boss Warren Joyce during his time coaching Manchester United’s youngsters, skipped into the area and referee Keith Stroud judged that he was tripped by Burn as he entered the penalty area, much to the anger of the Latics players and crowd.
Pitman took the responsibility from the spot and sent the ball low to Jussi Jaaskelainen’s left and into the net to claim his second goal - and second penalty - of the season.
Town continued to play with a freedom rarely seen this season and ought to have been two in front in the 12th minute when Wigan skipper Stephen Warnock gifted the ball to Lawrence on the edge of the box but the on-loan Leicester man’s touch let him down and Jaaskelainen claimed.
Moments later, Skuse sent Sears away on the left but the former West Ham man’s shot was blocked.
On 13 Pitman was yellow-carded for kicking the ball away as Wigan prepared to take a freekick on halfway, then three minutes later Dozzell joined him in the book for pulling back Michael Jacobs.
The home side forced Bartosz Bialkowski into action for the first time from the resultant freekick, Will Grigg diverting Jordi Gomez’s cross goalwards. However, Bialkowski reacted quickly to stick out a hand to stop it and in any case the linesman had raised his flag.
Wigan were starting to come more into the game and in the 22nd minute Bialkowski had to come off his line quickly to claim ahead of Max Power after a mistake by Adam Webster.
But the Blues were still largely on top and in the 26th minute, after Lawrence had crossed from the left following a corner, Dozzell hit a shot from the edge of the box which deflected wide. From the resultant flag-kick, Pitman flicked it on and the loose ball fell to skipper Luke Chambers, who hooked a volley well over.
There was a scare at the other end a minute later when Jacobs’s cross flicked off a Town player and found Grigg but Bialkowski claimed his header.
However, Wigan got back on terms in the 35th minute. Gomez’s initial freekick hit the wall but as he brought the ball away Sears was penalised for a high boot.
The second freekick was played short to Max Power, who smashed a shot goalwards. Bialkowski saved but could only knock the ball back into the danger zone and Wildschut netted the rebound from close range.
The goal gave Wigan and their fans a huge lift and the Latics went looking for a second. On 38 scorer Wildschut saw a strike blocked, then in the 41st minute Power skipped through the Blues midfield and hit a low shot which was destined for the corner of the net until Bialkowski somehow managed to get down to his right to palm it past the post.
In the final scheduled minute of the first half Kellett was booked for a foul on Williams but Lawrence’s ball into the box was cleared.
Burn joined him in the book in injury time for a high boot as Pitman sought to nod the ball into the area when he would have been through one-on-one.
After the initial freekick was cleared, Chambers sent the ball back in from the right and the ball eventually fell to Williams, who slammed a low shot against the post.
The ball stayed in play and Williams crossed back in from the left and the ball struck a Wigan player on his hand, according to vociferous and lengthy protests from the Town players. Referee Stroud only awarded a corner, then before Lawrence could take it Jaaskelainen talked himself into the book.
Soon after referee Stroud’s ended the half and was loudly booed off by home fans for the early penalty, although the Town players might have been equally aggrieved regarding the decision just before the end.
After starting very well and claiming their lead - even if the penalty may have been fortuitous - the Blues should have made their dominance count more and Lawrence will have been disappointed not to have taken his chance.
However, rather than continuing to grab the game by the scruff of the throat Town seemed to go into themselves and allowed Wigan back into the game.
And having got on terms the home side got themselves on top, although Williams was unlucky not to restore the lead when he hit the post and the Blues players seemed adamant they ought to have been awarded a second penalty just before half-time.
Wigan: Jaaskelainen, Kellett, Warnock (c), Buxton, Burn, Perkins, Gomez, Power, Jacobs, Wildschut, Grigg. Subs: Lavercombe, Byrne, Le Fondre, Davies, L Burke, Barrigan, Stubbs.
Town: Bialkowski, Chambers (c), Knudsen, Webster, Berra, Skuse, Dozzell, Williams, Sears, Lawrence, Pitman. Subs: Gerken, McGoldrick, Varney, Bru, Douglas, Ward, Kenlock. Referee: Keith Stroud (Hampshire).