Juan Mata's last-gasp winner moved Chelsea to within two points of the top four after Branislav Ivanovic's controversial opener set them on course for a 2-1 win over Wigan on Saturday.
Mata found himself in the right place at the right time to turn home from close range after Fernando Torres had fired a volley against the post in the third minute of stoppage-time at Stamford Bridge.
But it was Chelsea's first goal that sparked a furious reaction from Wigan, who were convinced the Serb was well offside when he turned home a Raul Meireles cross.
Referee Mike Jones ignored the protests of the visitors and awarded the goal after consulting with his assistant, although replays supported Wigan's claims that they had been hard done by.
Wigan's misery didn't end there and they left empty-handed after believing they had secured a deserved point after Mohamed Diame's 82nd minute effort had cancelled out Ivanovic's 62nd minute strike.
Chelsea are now up to fifth, above Newcastle on goal difference, and within two points of fourth placed Arsenal, who host Manchester City on Sunday.
The midweek Champions League quarter-final win over Benfica had kept the Blues' recent impressive run going and set up the tantalising prospect of a semi-final meeting with Barcelona.
But interim manager Roberto Di Matteo had attempted to re-focus his players' minds in the league ahead of this game by insisting a fourth place finish was still Chelsea's main target.
With a trip to local rivals Fulham looming on Monday, Di Matteo took the opportunity to rotate his squad, making seven changes from the side that started against Benfica.
Captain John Terry was an enforced absentee after revealing he has been playing recently with two cracked ribs while Frank Lampard and Ashely Cole were also injured.
But the wholesale changes did little to freshen up a side that looked as though it was still affected by the midweek efforts.
Wigan had already served notice they have no intention of slipping out of the Premier League without a fight and came into this clash on the back of successive wins over Liverpool and Stoke.
It took Chelsea 22 minutes before they managed to threaten Ali Al Habsi's goal with Gary Cahill forcing a good save from the Wigan keeper with a long-range effort.
But Cahill was involved in a scare inside his own area when Wigan claimed Shaun Maloney's cross had been blocked by the centre back's arm in the 28th minute.
Three minutes later, Chelsea lodged their own claim for a spot-kick when Didier Drogba was held by Gary Caldwell.
Drogba should have scored in the 35th minute when his header was cleared off the line by Maynor Figueroa after Al Habsi had blocked Mata's close range shot.
Then on the stroke of half time he connected with a far post header that drew another fine save from Al Habsi.
Di Matteo's side took the lead thanks to a major slice of luck in the 62nd minute when referee Mike Jones decided Ivanovic was onside when he side-footed home from Meireles's cross.
Wigan were convinced the Serb was offside and television replays appeared to support their case.
But the goal stood and 60 seconds later Ivanovic made another telling contribution, this time at the other end when he cleared Franco Di Santo's effort off the line.
Wigan found a way back into the game through substitute Diame who created space for himself on the edge of the area before lashing home a left foot drive, but Mata had the last word with his close-range winner following Torres's volley.