Sergio Aguero’s 90th minute winner sealed three points against the 10-men of Bayern Munich after Medhi Benatia was sent off after 21 minutes.
Aguero opened the scoring from the penalty spot then Xabi Alonso and Robert Lewandowski took the lead for Bayern before Aguero struck two late goals past Manuel Neuer.
Manchester City started brightly in a frantic first 30 seconds that saw Samir Nasri cuts inside from the left after being played and his shot is blocked on the edge of the area.
Gael Clichy produced a bursting run forward from the left resulting in a cross towards Frank Lampard who headed over from 10 yards.
A vital save from a spread-eagled Joe Hart prevented Sebastian Rode from opening the scoring on 9 minutes after a delicately chipped through ball from Arjen Robben.
Shortly after, Robben fired powerfully, yet harmlessly, wide of Hart’s near post as he cut in from the right wing onto his favoured left foot.
Robben’s pace saw him reach the byline on the left and his pull back found Rafinha whose thunderous shot was blocked by Clichy.
Aguero found himself through on goal after a Frank Lampard through ball and when Benatia fouled him inside the penalty box, Czech referee Pavel Kralovec pointed to the spot and sent off the defender.
Aguero stepped up to the penalty and side footed the ball past the enourmous frame of Neuer and into the right hand side of the goal.
Sebastien Rode’s full Champions League debut came to an end 24 minutes in as Pep Guardiola sacrificed him for another defender, Dante.
Lewandowski’s side step past Elaquim Mangala brought about a free kick on the edge of Manchester City’s penalty area and Alonso took up and struck past a motionless Hart into the bottom right corner.
Bayern took the lead just before half time when Rafinha’s cross reached Lewandowski and his combination of head and shoulder looped the ball over Hart and into the back of the net.
The second period started with Alonso wasting a glorious chance during a heavily numbered Bayern counter-attack which saw his left footed shot fly over the bar.
Lampard played Jesus Navas into some space down the right side and his low, powerful shot from a tight angle was comfortably saved by Neuer, then James Milner’s bending effort from the left hand side lacked the required curl on it.
Aguero’s lay off to Lampard produced a rasping drive from range which was heading for the net but for a strong hand from Neuer.
Captain Vincent Kompany tried guiding his team back into this contest with a volleyed effort from an outswinging Nasri corner, but it trickled out for a goal kick.
Jovetic pounced on a loose Alonso pass which sets free Aguero whose left footed finish slid past Neuer with aplomb and draw City level.
Then, in the 90th minute Aguero stole the ball from Boateng and drove the ball past Neuer to seal his hat-trick and the three points.