European champions Bayern powered to a convincing victory at the Etihad Stadium on Wednesday night.
The formidable attacking trio of Franck Ribery, Thomas Muller and Arjen Robben all struck as City were completely outplayed in Champions League Group D, although they also contributed to their own downfall.
Errors from goalkeeper Joe Hart and the defense proved costly but the hosts at least finished strongly as Alvaro Negredo replied and Bayern had former City defender Jerome Boateng sent off.
The result lifted Bayern clear at the top of the group and, even after just two games, probably left City in a battle for second place with their next opponents CSKA Moscow.
Bayern coach Guardiola, who has remarkably faced criticism despite an unbeaten start to the Bundesliga season, fancies City to progress and said: "I said it yesterday and nothing changed my mind.
"They are going to qualify and will be a tough opponent for the next round, but I can only talk about my team and what they did."
The former Barcelona boss added: "I am respectful when you play against Manchester City with these unbelievable players.
"We played better, we won, but the football is special.
"I am lucky to be here to train these players.
"It is nice for the team to come to this country, where they love football so much, and play like we did today."