The champions looked to have blown a 2-0 lead when two-goal Emile Heskey deservedly put Wigan back on level terms at the JJB Stadium, only for Arjen Robben to conjure a stoppage-time winner with his first goal of the season.
The victory keeps Chelsea breathing down the necks of Premier League leaders Manchester United, who ran out 3-0 winners at Aston Villa earlier thanks to two goals from an inspired Cristiano Ronaldo and a memorable volley from Paul Scholes.
Going into the hectic holiday fixtures, Chelsea trail United by two points. United have 47 points and no team with at least that many at the halfway stage has failed to win the title.
"I'm not proud of them (the players)," manager Mourinho told Sky Sports. "Father Christmas must wear blue because we didn't deserve to win.
"We were in complete control but with 15 minutes to go in the first half I could smell it (Wigan's comeback)...passing the ball bad, losing position, losing balance, conceding a goal in the last second of the first half.
BRILLIANT ATTITUDE
"Wigan had a brilliant attitude," added Mourinho, who said his team were not the same without captain John Terry (back injury).
"I must give credit to the players because in the last 10 minutes they put a lot of pressure on Wigan. But we did not deserve these three points and Wigan must be very disappointed."
Chelsea were cruising after Robben put in Frank Lampard for the opener and Salomon Kalou headed the second. Heskey then restored parity as the champions threatened to implode.
"It seems like we don't like easy matches," said Mourinho. "Some of the players were complacent...when we finished like we finished how can we play so bad for 25 minutes?
"The worst thing for me is when you have things in your hands but you waste it."
His United counterpart Alex Ferguson could not have been more content, even if Chelsea's late winner would have taken the gloss off his evening.
"It was a fantastic performance against a very good Villa team," Ferguson said after his side made amends for last week's 1-0 defeat by West Ham United.
"We are definitely top at Christmas and that just goes to show you can't listen to Jose (Mourinho) too much because he said we wouldn't be there at Christmas."
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