The City boss made seven changes for the game, a continuation of the rotation policy he has employed for much of the campaign.
But Leeds produced a determined performance, scoring the winner on the counter despite playing the second half with 10 men.
It was only our second defeat in our last 29 matches across all competitions and we remain on course to win four trophies in the final months of the season.
Guardiola, whose side now head to Germany for Wednesday's Champions League quarter-final second leg against Borussia Dortmund, says every single player at the Club has his faith – and if they didn’t, they would not be selected.
“When you lose [the team selection is a mistake], when we win, I am a genius,” he said afterwards.
“I do not regret [the selection] because I trust them. If I didn't trust them, they would not play.
“Everyone was good. It was a game of transitions. We had to avoid it, they did it.
“At 10 v 11, we need inspiration and we can't let them run [from deep]. We did it for a long time but then Raphinha had a chance and Eddie saved - and then they scored.
"When you attack and attack and attack, you have to control and not let them run."
City went behind late in the first half when Stuart Dallas fired home from the edge of the area, and seconds before half-time Leeds were reduced to ten men when Liam Cooper was shown a straight red card.
We dominated the second period but failed to create clear chances and were caught on the counter when Dallas added a second in the closing moments.
It was a tactical masterclass from Marcelo Bielsa, and afterwards Pep sent his congratulations to the visitors.
“Congratulations to Leeds, first of all,” he said.
"We did not create enough for the forwards. It is part of the game.
"In the last 10 minutes they had other chances, they are fast and can do it. When they defend in the way they were doing you have to stop them running and we did not do that.
"We are going to rest and prepare two days for the game in Dortmund and decide on how we are going to play."