Although City initially appeared to be in good shape against the German giants, two Mario Gomez goals in eight first-half minutes turned the tie on its head.
Then, when Mancini introduced Nigel de Jong for Edin Dzeko 10 minutes after the re-start, the Bosnian seemed to exchange words with his manager. This drew Carlos Tevez into the row, with suggestions that the Argentina star, left stewing on the bench on Saturday, had refused to warm-up, which then led to an exchange with compatriot Pablo Zabaleta.
City could have had the perfect start when David Silva went down under a rather impetuous challenge from Jerome Boateng, it looked a certain penalty but the referee was unmoved.
Bayern took their time to get going but when they did they might have gone in front if Franck Ribery had got a touch to Thomas Muller's low cross.
Ribery blazed over before City were fortunate to survive getting in a real mess as they tried to play offside when Muller crossed, leaving Bastian Schweinsteiger completely free barely six yards out. Amazingly, the midfielder scooped his shot over.
But shortly after Bayern went ahead when Ribery lashed a fierce shot goalwards that Joe Hart could not hold. Somehow, Hart prevented Muller tucking home the rebound. But he could not stop Gomez making it third-time lucky as he finished from close range.
Aguero was booked for a foul on Schweinsteiger as City tried to steady the ship, but worse was to come in stoppage time when Toni Kroos fizzed over a free-kick that Van Buyten flicked goalwards. Again, Hart saved. Again, Bayern had another option as Gomez tucked home his second.
Bayern continued to press after the break as Muller met Philipp Lahm's cross at the near post but could not turn the ball goalwards, then Kolo Toure headed a dangerous Schweinsteiger corner away from the City box.
Kolo Toure was booked as he gave away a free-kick which would have led to a third Bayern goal if Hart had not superbly turned Gomez's header away.
Source: PA
Source: PA