The Premier League side ended the European champions' record run of 10 consecutive Champions League wins, although Guardiola's men held on to top spot in Group D.
Goals from David Silva, Aleksandar Kolarov and James Milner cancelled out efforts from Thomas Muller and Mario Gotze at the Allianz Arena, as the visitors recovered brilliantly from going 2-0 down.
Guardiola called for some perspective, though.
"Congratulations to Manchester City but congratulations also to my players who have qualified as group winners for the next round," he said.
"Defeat is never good, but maybe this club, the team and the coach needs a defeat to know how difficult it is to win the games - in the Bundesliga and in Europe.
"We are a great team but we can sometimes lose, because other teams have good players and good coaches."
Muller explained that the loss showed that even the defending European champions have their flaws.
"The human being in us came through today," he said.
"We were complacent. It's not like we let them have one chance after another but we didn't look good as a team conceding those goals."
