After a first half notable mainly for a serious-looking injury to James McCarthy, it was the hosts who took the lead with 59 minutes gone as a lovely move involving Charles N'Zogbia and Franco Di Santo ended with Hugo Rodallega beating Jussi Jaaskelainen.
But Bolton took only seven minutes to get back on level terms, Johan Elmander netting his fifth goal of the season, as the Trotters made it five games unbeaten and Wigan four.
Wigan boss Roberto Martinez handed goalkeeper Chris Kirkland his first start since August because current number one Ali Al Habsi was ineligible for the clash against his parent club, but there was little to worry the former England man in the first half.
Bolton were much the better side in the early stages but could not manage an effort on target. England new boy Kevin Davies had a couple of half chances with a header and an acrobatic volley, but both flew over the bar.
Wigan were limited to sporadic counter-attacks, and with half an hour on the clock Martinez was forced to make a substitution after McCarthy sustained what looked a serious injury.
The midfielder was tackled from behind by Fabrice Muamba, who was not even booked for the challenge, and received several minutes of treatment before being carried from the pitch.
Mohamed Diame came on in his place and slowly the pattern of the game began to change.
In the 35th minute, N'Zogbia came within inches of opening the scoring when he broke into the area on the right and curled a shot just past Jaaskelainen's far post.
The Finn then had to be alert to keep out Rodallega, who, after a surging run from left to right, probably should have done better than shoot straight at the keeper.
Wigan piled on the pressure as half-time approached and Jaaskelainen held onto another effort from the Colombian before N'Zogbia engineered a great shooting opportunity on the right but saw his effort blocked by Gary Cahill.
The home side picked up where they had left off in the second half, with Maynor Figueroa picking out Rodallega and the striker blazing his shot well over Jaaskelainen's bar.
But, if the striker might have done better then, he certainly made it count just before the hour mark as Wigan took the lead with a goal of real quality.
N'Zogbia set off on a run through midfield before playing in Di Santo, who may have been just offside, on the right. The former Chelsea man neatly diverted the ball into Rodallega's path and this time the striker was clinical.
The hosts just about deserved their lead and it was now up to Bolton to try to rediscover their early dominance.
Trotters boss Owen Coyle brought on Matt Taylor and Premier League debutant Rodrigo Moreno in place of Martin Petrov and Lee Chung-Yong with 65 minutes gone, and within a minute the visitors were level.
Stuart Holden's cross from the right was headed into the middle by Davies where Taylor's first contribution was to poke the ball into the path of Elmander, who slotted under Kirkland.
The game was now a much more even affair and, after Rodrigo tested Kirkland at his near post, Paul Robinson produced a brilliant tackle to halt another N'Zogbia run.
The ball ran to Di Santo and the Wigan fans thought he had put them back in front as his shot rippled the side-netting.
It was then Rodallega's turn to miss the target, and only the Colombian will know how he failed to score as he rose to meet Jordi Gomez's corner five yards out.
With eight minutes left, Martinez made his final change, bringing on Tom Cleverley for Gomez, and the on-loan Manchester United midfielder made an immediate impact.
First he headed just wide when the Bolton defence inexplicably failed to challenge six yards out before forcing Jaaskelainen into a save with a fierce shot from the edge of the box.
The game ended with Wigan centre-backs Steven Caldwell and Antolin Alcaraz needing to be separated after a heated exchange, but they were at least able to celebrate a point gained.