Possesion dipegang oleh Man City 83% Wigan hanya 17%
City were reduced to 10 men following Fabian Delph's red card on the stroke of half-time, despite referee Anthony Taylor initially appearing to produce a yellow car
Wigan striker Will Grigg then scored the only goal of the game to knock City out of the FA Cup.
In doing so the Latics replicated their famous 1-0 victory over the same opposition in the competition's 2013 final.
Chaotic scenes followed the final whistle as Sergio Aguero appeared to confront a supporter who had invaded the pitch.
Guardiola found defeat hard to swallow after his side had dominated the game with 83 per cent possession.
Speaking to BBC Sport, the City boss said: "It was like a final.
"They had one shot on target, I don't have regrets with the way we played, the performance, the heart.
"Congratulations for Wigan for the qualification.
"We did absolutely everything, we made a mistake and this kind of game is like a final.
Pep Guardiola stares at the ground following Man City's shock defeat to Wigan
"Wigan won, congratulations to them and now we rest to prepare for the League Cup final."
Guardiola refused to be drawn on the referee's decision to dismiss Delph for a reckless tackle on Wigan's Max Power.
He did not criticise Taylor's choice of card, simply stating: "Red card. It was the decision."
On an apparent clash with Wigan boss Paul Cook in the tunnel he added: "Nothing happened."
Tonight was only the third time Manchester City have failed to score in a match this season.
Lower league sides have been responsible for two of those games, a 0-0 draw with Wolves in the Carabao Cup being the other.
