Guardiola believes Manchester City's 'new generation is coming' after Bayern win
James McAtee - who spent last season on loan at Championship side Sheffield United, making 37 appearances and scoring nine times to help the club secure promotion to the Premier League - opened the scoring for City in the 21st minute in Tokyo.
Fellow youngster Oscar Bobb also showed flashes of his quality after coming on as a second-half substitute in the 2-1 victory.
Rico Lewis was the standout performer though, constantly causing Bayern problems going forward and not shying away from his defensive duties in the middle of the park.
Speaking to reporters after the game, Guardiola said 18-year-old Lewis was "so smart, so intelligent".
"He understands everything and is reliable in many, many things," he said of the player who made 14 appearances in the Premier League last season.
"We are really, really pleased a player from the academy came up and is playing the way he is playing."
Guardiola - himself a graduate of Barcelona's famed La Masia academy - expressed his pride at the quality of players City were now producing, declaring "the new generation is coming".
Guardiola also praised the way in which the academy was benefiting City's finances, pointing out that "we sell a lot, with a buy-back (clause) normally".
"So just for the academy in two transfer windows here £80 million, or £85 million, is just unbelievable," he said.
"I'm pretty sure one or some of them maybe in the future will be back here with us. So yeah, really pleased."
Bayern manager Thomas Tuchel responded to more questions about his club's pursuit of Tottenham Hotspur striker Harry Kane, saying "I have nothing to hide".
"I'm looking for a player because we have a lot of injured players, and we have a difficult situation," Tuchel said.
"However, having said that, we made a lot of opportunities today and in terms of how to build the match I think we did well."
Aymeric Laporte wrapped up the win for City in the 86th minute after Mathys Tel levelled for Bayern five minutes earlier.