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.
We lacked the finishing touch - Villas-Boas
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.
Martinez thinks Wigan should have won
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.
Full Time The referee signals the end of the game.
Salomon Kalou takes a shot. Ali Al Habsi makes a save.
Free kick awarded for a foul by Franco Di Santo on Mikel. Direct free kick taken by Raul Meireles.
Headed effort on goal by Franco Di Santo from inside the penalty box misses to the right of the goal.
Ronnie Stam delivers the ball, Franco Di Santo produces a header from the edge of the box and misses to the right of the goal.
The assist for the goal came from Hugo Rodallega.
87:16 Goal scored
Goal! - Jordi Gomez - Wigan 1 - 1 Chelsea Jordi Gomez fires in a goal from close in low into the middle of the goal. Wigan 1-1 Chelsea.
Hugo Rodallega takes a shot. Save by Petr Cech.
Mohamed Diame gives away a free kick for an unfair challenge on Mikel. Direct free kick taken by Petr Cech.
Florent Malouda produces a left-footed shot from the edge of the box and misses to the right of the goal.
Victor Moses is flagged offside by the assistant referee. Petr Cech takes the free kick.
Effort from outside the penalty box by Franco Di Santo goes wide left of the target.
Ronnie Stam produces a cross, Frank Lampard manages to make a clearance.
Petr Cech restarts play with the free kick.
Substitution Florent Malouda on for Daniel Sturridge.
Hugo Rodallega challenges Frank Lampard unfairly and gives away a free kick.
Corner taken left-footed by Jordi Gomez from the left by-line to the near post, Didier Drogba manages to make a clearance.
Franco Di Santo takes a shot. Branislav Ivanovic manages to make a clearance.
Substitution (Wigan) makes a substitution, with Franco Di Santo coming on for Conor Sammon.
Substitution Hugo Rodallega on for David Jones.
David Jones takes the outswinging corner, save by Petr Cech.
Outswinging corner taken by David Jones from the left by-line, Effort from deep inside the area by James McCarthy misses to the right of the target.
Free kick awarded for a foul by Didier Drogba on Gary Caldwell. Gary Caldwell takes the free kick.
Frank Lampard challenges Jordi Gomez unfairly and gives away a free kick. Direct free kick taken by Maynor Figueroa.
Substitution Juan Mata leaves the field to be replaced by Mikel.
Maynor Figueroa takes a shot. Save by Petr Cech. Short corner taken by Mohamed Diame.
Long range shot by David Jones goes wide right of the net.
Assist on the goal came from Ashley Cole.
58:04 Goal scored
Goal! - Daniel Sturridge - Wigan 0 - 1 Chelsea Daniel Sturridge finds the back of the net with a goal from close range to the bottom left corner of the goal. Wigan 0-1 Chelsea.
Juan Mata fouled by James McCarthy, the ref awards a free kick. Free kick taken by Branislav Ivanovic.
Shot by Didier Drogba from deep inside the penalty area misses wide to the left of the target.
Free kick awarded for a foul by Maynor Figueroa on Juan Mata. Free kick taken by Juan Mata.
Close range shot by Victor Moses misses to the left of the goal.
Outswinging corner taken by Juan Mata, clearance made by James McCarthy.
Jose Bosingwa sends in a cross, Gary Caldwell makes a clearance.
Maynor Figueroa takes a shot. Save by Petr Cech.
Inswinging corner taken by Frank Lampard from the left by-line played to the near post, James McCarthy manages to make a clearance.
Salomon Kalou takes a shot. Mohamed Diame gets a block in.
Jordi Gomez has a shot on goal from long range that goes wide left.
The referee blows his whistle to start the second half.
Substitution Salomon Kalou is brought on as a substitute for Oriol Romeu.
45:00 +1:14 Half time
Half Time The ref blows to signal half-time.
Raul Meireles has shot on goal from just outside the penalty box which goes wide of the right-hand upright.
Raul Meireles gives away a free kick for an unfair challenge on Victor Moses. David Jones takes the free kick.
Unfair challenge on Raul Meireles by Conor Sammon results in a free kick. Petr Cech restarts play with the free kick.
Victor Moses takes a shot. Branislav Ivanovic gets a block in.
Corner taken left-footed by David Jones.
Close range headed effort by Didier Drogba goes wide of the left-hand upright.
Raul Meireles takes a shot. James McCarthy gets a block in.
Foul by Conor Sammon on Branislav Ivanovic, free kick awarded. Petr Cech takes the direct free kick.
Effort from the edge of the box by Mohamed Diame goes wide of the right-hand upright.
Corner taken by David Jones from the right by-line, save made by Petr Cech.
The ball is swung over by Jose Bosingwa, Gary Caldwell makes a clearance.
Conor Sammon takes a shot. Blocked by John Terry.
The ball is crossed by Didier Drogba, clearance by Maynor Figueroa.
The ball is swung over by Jose Bosingwa, clearance by David Jones. Oriol Romeu has an effort at goal from 25 yards. Ali Al Habsi makes a save. Outswinging corner taken from the left by-line by Juan Mata, Maynor Figueroa manages to make a clearance.
Short corner taken by Juan Mata.
The referee blows for offside against Didier Drogba. Ali Al Habsi takes the free kick.
The referee penalises Antolin Alcaraz for handball. John Terry takes the indirect free kick.
Foul by Raul Meireles on Jordi Gomez, free kick awarded. Gary Caldwell takes the free kick.
Corner taken by Juan Mata, clearance by James McCarthy.
John Terry takes a shot from a long way out which goes wide of the right-hand upright.
The ball is delivered by Juan Mata, David Jones manages to make a clearance.
Daniel Sturridge produces a cross, clearance made by Gary Caldwell.
Daniel Sturridge crosses the ball, clearance made by Gary Caldwell.
Foul by Branislav Ivanovic on Victor Moses, free kick awarded. Gary Caldwell takes the direct free kick.
Short corner worked by Victor Moses.
Foul by Ronnie Stam on Juan Mata, free kick awarded. Juan Mata takes the direct free kick.
Raul Meireles gives away a free kick for an unfair challenge on Jordi Gomez. David Jones restarts play with the free kick.
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