Pep Guardiola used his substitutes brilliantly as Julian Alvarez and Jeremy Doku came off the bench to win the game late on in Germany.
Defending champions City dominated the match throughout but, at 1-1, were still looking for a vital second with the clock ticking down in the second half.
But Alvarez curled home a beautiful strike on 84 minutes to put us 2-1 ahead and Doku sealed the three points as he finished expertly in the second minute of added time.
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Earlier, Phil Foden had opened the scoring with a fine right foot finish on 25 minutes before Lois Openda levelled matters on 48 minutes against the run of play.
The result ensured a maximum six points from two games so far in Group G.
Watch our highlights in the video player above.