This all occured without the assistance of Mario Mandžukić.
In an effort to rotate his squad, Bayern manager Pep Guardiola pushed Thomas Müller up top, creating a dynamic front five that confounded the Sky Blues.
"Of course someone can say: 'City was not very well organized,'" said Arjen Robben. "But we used the space very well. There were attacks by us that were really good."
Franck Ribery struck first in the 7th minute, cutting inside of Jesús Navas and unleashing a 20-meter blast that Joe Hart could not handle. That gave FC Bayern an early advantage for the second consecutive Champions League match in a row.
FC Bayern controlled the pace of the first half, holding around 65 percent of the possession. Manchester City tried some runs through the Bayern back line, but were caught offside four times before halftime.
"I cannot remember having that much possession and that much ball demand in a foreign stadium agaisnt a well-known team," said Bayern president Uli Hoeneß. "I can only congratulate the team and the manager."
Manchester City took the game more to FC Bayern in the second half, pushing higher up the field and collecting two quick corner kicks. The defending champions held strong through the middle, even if it meant Manuel Neuer coming off his line to slice away a long through ball from Yaya Touré before Edin Džeko could get on the other end.
The more the sky blues pushed forward, the more vulnerable they became at the back. Müller recognized the high line from City's backs in the 56th minute, and called for a ball over the top. Dante saw his teammate begin to break and fluttered a pass over the opposition defense. Müller broke, collected the ball, dribbled around Hart and finished with his left foot in an unguarded net.
"Everyone can see that [the result] was richly deserved," said Müller. "It makes me happy how the team played football."
Fernandinho tried to get his team to break forward, but foolishly relinquished the ball to Toni Kroos in the 59th minute. Kroos found a breaking Robben on the right, and the Dutch winger took it from there. Streaking foward, Robben nutmeg-ed the on-coming Matija Nastasić and punished a shot off of Hart's outstretched arm and inside the right post to put Bayern up 3-0.
Álvaro Negredo salvaged some hope for the home side, providing a nice shift off the bench late in the second half. He scored on a cutback past Jérôme Boateng in the 80th minute to bring City back within two goals. He added a header off of a James Milner cross in the 89th minute that squirted just wide of the left post.
"We made it hard for ourselves again in the last ten minutes," said Müller. "There one sees Manchester City has very good individual class."
Boateng's tough return to the Etihad continued, coming in with a late challenge on Touré in the 86th minute. Referee Björn Kuipers deemed the foul a goal scoring opportunity, and sent off Boateng with a red card. That marks the second time in two years that Boateng has been showed red in the Group stages of the Champions League.
Bayern leaves Manchester not only with two-thirds of the possession and eight shots on goal, but also with an important six point swing in their favor. Manchester City is now second in Group D, their goal differencial separating them from PFC CSKA Moskva, who won 3-2 against Viktoria Plzen earlier in the afternoon.
"We are happy that we have six points," said Ribéry. "That is super. We need to continue just as concentrated."
1:0 Ribéry (7')
2:0 Müller (56')
3:0 Robben (59')
3:1 Negredo (80')
Yellow Cards: Kroos (45') / Agüero (42'), Nasri (70'), Milner (75')
Red Cards: Boateng (86')
FC Bayern: Neuer; Rafinha, Boateng, Dante, Alaba; Lahm; Robben (Shaqiri 78'), Schweinsteiger (Kirchhoff 76'), Kroos, Ribéry (Götze 85'); Müller
Manchester City: Hart; Richards, Kompany, Nastasic, Clichy; Touré, Fernandinho; Navas, Agüero (Silva 70'), Nasri (Milner 70'); Dzeko (Negredo 57')