The reigning German and European champions looked set to run riot at the Allianz Arena when Thomas Muller and Mario Gotze scored inside the first 12 minutes to give them a two-goal advantage.
However, David Silva pulled one back for City before the interval and second-half goals from Aleksandar Kolarov and James Milner completed a stunning turnaround.
Bayern's only previous loss under Guardiola came in July when Borussia Dortmund claimed a 4-2 victory in the German Super Cup.
Yet Lahm was able to take consolation from the team retaining top spot in Group D.
"You have to play better than we did today after you take a two-goal lead," said Lahm. "However, we won the group and that was our main target."
Meanwhile, Guardiola believes that City's comeback may even benefit Bayern in the long run.
"Congratulations to Manchester City on this great victory," said the Spaniard. "I hope that we understand how difficult it is to play in Europe on occasions - it seems we sometimes need to lose a game.
"Now we have to cope with that defeat."
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