Jordi Gomez's late equaliser halted Chelsea's charge up the Premier League table and gave Wigan a vital point in their relegation battle.
The Latics felt they should have had a first-half penalty when Victor Moses' shot struck Branislav Ivanovic's arm.
Chelsea improved after the break and took the lead when Daniel Sturridge fired home from Ashley Cole's pass.
But Wigan refused to give up and denied the Blues victory when Petr Cech's fumble gifted Gomez a simple tap-in.
A point was exactly what Wigan deserved after refusing to be intimidated by Chelsea's lofty status, matching the Londoners stride for stride.
Sturridge's superb finish looked to have set Chelsea on course for their fourth straight league win, but Wigan continued to attack and boss Roberto Martinez's decision to bring on strikers Hugo Rodallega and Franco Di Santo proved inspired as the duo combined to set up Gomez's late goal.
The setback leaves Chelsea third in the table, six points behind leaders Manchester City, who host Arsenal on Sunday.
Wigan, meanwhile, are now just one point behind Wolves, who lost to Stoke, in 17th after picking up seven points in their last four games.
Indeed, the Latics began the game with the confidence of a team in good form and had an early penalty appeal turned down when Gomez went down in the box under Cole's challenge.
DID YOU KNOW?
Wigan had conceded 15 goals without reply in their previous three league meetings with Chelsea
Chelsea slowly passed their way into the match, but chances were few and far between as Wigan defended with impressive resolve.
Unable to pierce the home side's rearguard, the Blues were restricted to shots from distance, with captain John Terry fizzing wide from 30 yards and Oriol Romeu cracking a low volley which Ali Al Habsi tipped around the post.
The best opportunity of the half went Chelsea's way five minutes before the break when Raul Meireles picked out Didier Drogba six yards out, but the striker's diving header went wide.
Then came the most controversial moment of the half, as Wigan were denied a penalty when Moses' drive hit Ivanovic on the arm.
Replays suggested the Serb moved his arm towards the ball to block the goal-bound effort, but referee Martin Atkinson remained unmoved.
Chelsea boss Andre Villas-Boas brought on Salomon Kalou at half-tim, and the Ivorian made an immediate impact on the left, getting to the byeline and cutting back for Drogba to fire into the side netting.
Wigan survived that scare but could not prevent the visitors from taking the lead through the consistently-impressive Sturridge.
Cole picked out the run of the England striker, who took one touch to control the ball with his left foot before drilling his fourth goal in five league games right-footed past Al Habsi.
Wigan desperately searched for a response. Maynor Figueroa fired in a shot that was destined for the bottom corner until Cech stretched out a hand to push it wide.
Then a sloppy backpass from Ivanovic gave substitute Rodallega a sight of goal. His effort was smothered by Cech, but the ball fell to Di Santo, whose shot was cleared off the line by Ivanovic.
Still the Latics poured forward and they gained their reward three minutes from time when Rodallega's shot was spilt by Cech straight into the path of the grateful Gomez.
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