Arjen Robben's dramatic stoppage time strike kept Chelsea in touch with league leaders Manchester United.
Robben made two goals and scored one
The Dutchman's neat pass set up Frank Lampard to score Chelsea's first and then Salomon Kalou headed in Robben's outswinging corner for the second.
But just at the end of the first-half Emile Heskey's header reduced the deficit when he guided in a free-kick.
Heskey turned the ball in from close range to equalise for Wigan, but Robben had the last word with a raking shot.
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Last weekend Chelsea had beaten Everton 3-2 at Goodison Park, with their winner coming in the 87th minute.
This time Chelsea left it even later as Robben's goal kept them just two points behind United.
Chelsea were ruffled by Wigan's dynamic second-half performance and until Robben's late intervention Paul Jewell's side looked destined to come away with at least a point.
Wigan's spirit was encapsulated by Heskey, who had scored only three league goals this season before this match, but single-handedly terrorised the Chelsea defence.
Chelsea must be wondering why they had to leave it so late to win this game given their almost total control of the opening period.
Kalou, who was preferred to Andriy Shevchenko, had two reasonable chances to score before Lampard gave Chesea a 12th-minute lead.
The former Feyenoord striker first tested Chris Kirkland with a flicked effort after he collected a long pass from Ashley Cole.
Kalou then got on the end of a rapier-like Chelsea counter-attack inspired by Didier Drogba and Robben.
Kalou's stabbed effort sneaked under Kirkland's glove to hit the post, but the Wigan goalkeeper beat the Chelsea striker to the rebound.
But Chelsea were not to be denied for much longer.
There seemed little danger as Robben lurked on the edge of the box, but the Dutchman conjured up a wonderful reverse pass to leave Lampard in acres of space with just Kirkland to beat.
This time Kirkland was unable to do keep the ball out, as Lampard crashed a shot past the Wigan goalkeeper.
In the 30th minute Kalou was the first to the ball following a Robben corner and his header was too strong for Kirkland as he made it 2-0.
Wigan came back into the game towards the end of the first half and Heskey's header revived the home side's hopes.
Heskey won the free-kick, tempting Khalid Boulahrouz into a rash challenge, and the former Liverpool striker then got to Josip Skoko's set-piece delivery before Drogba.
Immediately after the restart Lampard uncharacteristically passed up an opportunity to restore Chelsea's two-goal lead, when having left a couple of Wigan defenders on their backsides the midfielder fired wide.
Chelsea were left to rue that miss when Heskey was on hand to direct the ball into the roof of the net after Denny Landzaat turned back David Cotterill's cross from the right.
In a frenetic finale Kirkland did well to tip over Ricardo Carvalho's header, but the Wigan goalkeeper could do nothing about Robben's left-footed shot.
Wigan manager Paul Jewell:
"I don't like unlucky teams as they get relegated - we have to start turning those good performances into points.
"I don't think we will get relegated, but I feel flat and we have to pick ourselves up.
"We've pushed Chelsea all the way and we deserved something from this game."
Chelsea manager Jose Mourinho:
"I'm not proud, I'm very sad. We don't deserve to win this game.
"We won because we had a good reaction in 10 minutes.
"This was our easiest game to win. After the way we started we had control of the game. It looks like the team is comfortable in difficult situations."
Wigan: Kirkland, Boyce, De Zeeuw, Hall, Baines, Johansson (Cotterill 72), Skoko, Landzaat (Wright 84), Kilbane, Heskey, Todorov (Teale 77).
Subs Not Used: Pollitt, Jackson.
Booked: Heskey, De Zeeuw, Kilbane.
Goals: Heskey 45, 75.
Chelsea: Hilario, Essien, Boulahrouz (Shevchenko 79), Carvalho, Ashley Cole, Lampard, Makelele (Mikel 79), Ballack, Kalou, Drogba, Robben (Geremi 90).
Subs Not Used: Hedman, Bridge.
Booked: Robben, Boulahrouz, Lampard, Mikel.
Goals: Lampard 13, Kalou 31, Robben 90.
Ref: M Dean (Wirral).