The predatory German striker opened the scoring after Joe Hart denied both Franck Ribery and Thomas Muller with instinctive saves, but the England keeper could not repel the 26-year-old's effort.
On the stroke of half-time, Tim Kroos's free-kick was nodded goalbound by Daniel van Buyten. Hart palmed his effort away, but once again Gomez was first to react and prodded home, much to the ire of the City keeper.
More to follow.
Helpless: Joe Hart - who had denied Franck Ribery and Thomas Muller - can do nothing to repel Mario Gomez's close-range effort
MATCH FACTSBayern Munich: Neuer, Rafinha, Van Buyten, Boateng, Lahm, Schweinsteiger, Gustavo, Muller, Kroos (Tymoschuk 82), Ribery, Gomez. Subs not used: Butt, Petersen, Robben, Usami, Contento, Alaba.
Scorer: Gomez 38, 45+1.
Man City: Hart, Richards, Kompany, K Toure, Clichy, Nasri (Milner 69), Barry (Kolarov 73), Y Toure, Silva, Aguero, Dzeko (De Jong 55). Subs not used: Pantilimon, Zabaleta, Lescott, Milner, Tevez.
Yellow cards: Aguero, Clichy, K Toure, Y Toure.
Referee: Viktor Kassai (Hungary).
Two's up: Gomez reacts quickest to Hart's save from Daniel van Buyten's header to double Bayern's advantage
The agony and the ecstasy: Mullar looks aghast after seeing his effort saved by Hart, unaware that Gomez is about to give Bayern the lead
Losing it: Hart was apoplectic following Bayern's second goal
Tempers flare: Edin Dzeko hurls his boots at the ground following his substitution
The one that got away: Hart denies Gomez
No penalty: Micah Richards goes to ground in the box following Jerome Boateng's challenge
Kick shot: Sergio Aguero wins the ball from Van Buyten
Getting stuck in: Vincent Kompany steals possession from Gomez
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