Despite an impressive and brave showing by Mancini's side, the result didn't amount to much as a Napoli win sent the Eastland's team crashing out of the competition.
David Silva put his team in the lead with a terrific strike following a smart touch from Edin Dzeko, before Yaya Toure doubled City’s advantage after a nexus of intricate passes which resulted in the Ivorian calmly slotting home in the second half.However, goals from Gokhan Inler and Marek Hamsik for the Italians at Villarreal were enough to ensure that they maintained their one-point advantage over the English side to progress.
Jupp Heynckes made a eight changes to the Bayern side that beat Werder Bremen 4-1 at the weekend. Hans-Jorg Butt replaced Manuel Neuer in goal and Nils Petersen made his first Champions League start; Franck Ribery and Mario Gomez, however, started as substitutes.
City’s only chance early on came via a Samir Nasri cross which Sergio Aguero couldn’t keep down, seeing his header soar over the bar.
Then, at the other end of the pitch, Ivica Olic found himself free momentarily outside the box, but his low, driven shot was pummelled away by Joe Hart for a corner.
Mancini’s men began to dictate the tempo, dominating possession as Bayern struggled to get into the game.
City then took the lead via a stunning goal from Silva. The Spaniard was lurking at the edge of the area as Dzeko touched on Gareth Barry’s pass from the right wing. The ball sat up perfectly for the playmaker, who lashed the ball home into the bottom corner.
Aguero almost doubled his team’s lead moments later. Toure charged forward and found the striker who beat two defenders and evaded the keeper, only to see his shot cleared off the line by Jerome Boateng.
The effervescence of Aguero and Silva put continuous pressure on Bayern. The Spanish maestro went close to scoring his second as City clearly benefited from their opening goal. Silva wriggled between defenders inside the box and, after unleashing a shot which was parried away by Butt, the follow up was poked over the bar by Barry.
Both teams looked intent on scoring following the second-half kick-off. It was City, however, that proved the more efficient in attack as they cushioned their lead thanks to Toure.
An exquisite passing move by Mancini’s charges which saw Toure a play a one-two with Silva and then with Dzeko, resulted in the Ivorian finding himself free in the area to tuck the ball under Butt.
Attempting to get back into the game, Bayern created a half-chance - a Vincent Kompany header inside City’s area found David Alaba, whose left footed shot from outside the area was awkwardly parried away by Hart.
In the 65th minute the stadium fell quiet as news of a Napoli goal filtered through the masses, sending negative vibes across the stadium and was exacerbated as Bayern fans chanted ‘Napoli’.
The game lost its urgency as the news that the Naples outfit had doubled their lead filtered through yet the home side continued to push on for a third goal.
Johnson had a chance to finish the game off as Balotelli pushed forward into the box but, upon receiving the ball, the England international shot wide.
Manchester City must settle for Europa League football after Christmas, while Bayern can look forward to bringing back their first-team regulars as they aim to qualify for the final, being held in their very own Allianz Arena in May.