Chelsea, who had won their last three league matches and inlicted a first defeat of the season on leaders Manchester City on Monday, looked to be heading for another win after a superb 59th-minute goal by Daniel Sturridge, but Jordi Gomez capitalised on Cech's error to score for the home side in the 88th minute.
The result extended Wigan's recent revival after a run of eight successive defeats. They have now lost just one of their last five games, although they remain in the relegation zone.
While Spaniard Gomez scored his fouth goal in five matches, Chelsea's Spanish striker, Fernando Torres, who joined the club from Liverpool in January for a British record fee of 50 million pounds, was left on the bench for the second successive game.
Chelsea manager Andre Villas-Boas said afterwards: "It was a hard-fought game with many chances, maybe more from Wigan who fought hard to get a result.
"In the last moments if we'd have cleared the ball better maybe we'd be taking the three points away, but I think 1-1 is a fair result."
Wigan's manager, Roberto Martinez, whose side had conceded 15 goals against Chelsea in their preceding three league matches, said: "I was probably more delighted with the performance than the result.
"To have more corners, better possession and more chances than Chelsea, who are in a fantastic run of form, speaks volumes for my players. They were magnificent."
Chelsea were not the only leading team to stumble on Saturday, as Newcastle United's hopes of a top-four finish took another knock when they were held to a goalless draw at St James' Park by Swansea City and failed to win for the fifth successive game.
Newcastle's 11-match unbeaten run from the start of the season, which ended a month ago, now seems a distant memory.
