Will Grigg grabbed the winner for Wigan to end City's hopes of the Quadruple.
Guardiola stated: "Congratulations for Wigan for the qualification. We did absolutely everything, we made a mistake and this kind of game is like a final. OK, we accept the defeat. Congratulations to the winner.
"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. I judge my players on intentions and not results and the intentions were good.
"Wigan won, congratulations to them and now we rest to prepare for the League Cup final."
On Fabian Delph's red card, Guardiola said: "Red card. It was the decision."
The City manager also refused to discuss his halftime clash with Wigan manager Paul Cook.