James McAtee (second from the left) spent last season on loan at Championship club Sheffield United and helped them secure promotion to the Premier League
Midfielder James McAtee, 20, opened the scoring in the first half following good work from 18-year-old Rico Lewis.
Mathys Tel equalised for Bayern on 81 minutes before Aymeric Laporte restored City's lead five minutes later.
"It's unbelievable - the guys who are in charge and the recruitment," Guardiola told the club's website.
"The new generation is coming and they told me it is really good. There are three or four players that are exceptional."
City secured their second pre-season victory at Japan's National Stadium in front of another sellout crowd after the Treble winners came from behind to defeat Yokohama F Marinos 5-3 at the weekend.
Guardiola and his team travel to Seoul, South Korea to face Atletico Madrid at 12:00 BST on Sunday, before taking on Arsenal in the Community Shield on 6 August.
Academy graduate McAtee was able to tap in the rebound from Julian Alvarez's low shot that was saved by Bayern goalkeeper Yann Sommer after fellow graduate Lewis teed up the Argentina forward.
Bayern boss Thomas Tuchel sent out a fresh line-up for the second half, while City manager Guardiola made eight half-time changes.
Water breaks were also enforced midway through each half because of the sweltering heat in the Japanese capital.
French forward Tel pulled one back for German champions Bayern with nine minutes left before England midfielder Phil Foden nudged the ball into the path of Laporte to score a late winner.
Guardiola added: "We sell a lot [of players], normally with a buyback [clause]. To make £80m or £85m just from the academy is unbelievable.
"That shows how good the club is working. I am pretty sure that one or some of them maybe will be back here with us. [I'm] really pleased."
City beat Bayern in the quarter-finals of the Champions League on their way to lifting the trophy in June. They also celebrated winning their seventh Premier League title and the FA Cup during the 2022-23 campaign.
On how City look heading into the new season, Guardiola said: "The group is ready. No injuries - that is good. We are not far away but we are not in our best conditions.
"We will play the Community Shield not being in our top, top form. This is normal. We rely on the mentality that we have and the personality that we have.
"We have one week in Manchester to prepare for that final and train better than we can here."
-- Courtesy of BBC Sport