Alvaro Negredo finally got the better of Manuel Neuer on the hour-mark but the hosts hit back with goals from Thomas Muller and Mario Mandzukic to edge an entertaining match at the Allianz Arena.
After a day of searing heat in Munich, it was something of a relief this game started as the main course rather than the starter between Sao Paulo and AC Milan which merely encouraged an afternoon siesta.
Two games in little over 24 hours meant there was always going to be wholesale changes against Bayern and only Stevan Jovetic and Fernandinho remained from the starting XI that faced AC Milan.
In contrast, Bayern started with arguably their strongest side as Pep Guardiola sought some early silverware after losing out in the German Super Cup to Borussia Dortmund.
You’d have to say it showed too, especially in the first five minutes when the hosts peppered the Blues’ goal, usually at the promptings of Franck Ribery who forced Costel Pantilimon into a smart save with barely 60 seconds played.
Ribery then went close with a volleyed shot that went a foot wide but despite Bayern controlling much of the opening exchanges, City dug in at the back where Vincent Kompany and Dedryck Boyata impressed as a duo.
And whenever Bayern did find a way through, Pantilimon was more than a match as he repelled Arjen Robben and Thomas Muller’s long range efforts.
Gradually, City played their way into the game and before the break went close to opening the scoring on three occasions. First a counter-attack involving James Milner and Pablo Zabaleta saw the latter pick out Jovetic on the corner of the box with a smart cross-field pass. The Montenegrin cut inside and then whipped a shot inches wide of Manuel Neuer’s post.
Then Alvaro Negredo had two excellent chances to score his first City goal, first heading Nasri’s cross straight at Neuer from six yards and then as he glanced Milner’s cross inches wide.
Yaya Toure and Jesus Navas were introduced at the break for Gareth Barry and Jovetic and it was the Blues who continued to threaten with Nasri enjoying his more central attacking role and breaking clear to first see Neuer win a one-on-one duel and then the assistant referee rule out his neat finish for offside.
Then Navas whipped in a perfect cross for Negredo who again was denied by Neuer at point-blank range – the former Sevilla striker could easily have been completing an 11-minute hat-trick on another night!
Then, finally, it happened – and typically, it was the hardest of the lot! Negredo chased a long ball through, out-paced the last man and tucked the ball home with a low drive that struck the post and went in.
The lead, however, was short-lived – six minutes in fact - as Pablo Zabaleta was adjudged to have handled in the box and Thomas Muller made no mistake. Worse was to follow as Mario Mandzukic headed home from close range to make it 2-1 on 72 minutes. It was harsh to say the least but a reminder that you can never switch off against teams of this quality.
Late sub Edin Dzeko might have equalised in the final moments, but all in all, the Blues will head home with their heads rightly held high after a productive few days in Germany.