City got the victory they required over the Germans but were undone when Napoli beat Villarreal in Spain by the same scoreline to clinch second spot behind Bayern, who had already won Group A.
Napoli’s success broke the hearts of City fans who had been singing and dancing after goals from David Silva and Yaya Toure but they will now have to settle for the Europa League following Gokhan Inler and Marek Hamsik’s second-half goals in Villarreal.
CSKA Moscow beat Inter Milan 2-1 at the San Siro in Group B to qualify for the knockout stages alongside the Italians who had already navigated their way through to the last 16 for the eighth successive season.
Trabzonspor and Lille both fell out of contention with a 0-0 draw as the Turkish club finished third to grab a Europa League spot.
In Group C, Manchester United lost 2-1 in Basel and are now out of the Champions League, six years to the day that they last didn’t qualify for the second stage.
Benfica beat Otelul Galati 1-0 to top Group C and remain unbeaten as Basel join them in the Round of 16 with United finishing third.
And finally, Group D saw Real Madrid set a new club record of six successive victories in Europe courtesy of a 3-0 win at Ajax who fall out of the competition.
Lyon needed a big win and they got it with a 7-1 result at Dinamo Zagreb who led after going down to ten men, however, the French club powered to victory fuelled by the fastest-ever Champions League hat-trick by Bafetimbi Gomis who netted three times in seven minutes in the second half on his way to four goals.
2011/12 Champions League scores – match-day 6
Lille (FRA): 0
Trabzonspor (TUR): 0
Stadium Metropole, Lille
Benfica (POR): 1 (Oscar Cardozo 7’)
Otelul Galatia (ROM): 0
Estadio da Luz, Lisbon
Dinamo Zagreb (CRO): 1 (Mateo Kovacic 40’, red card: Jerko Leko 28’)
Lyon (FRA): 7 (Bafetimbi Gomis 45’/48’/52’/70’, Maxime Gonalons 48’, Lisandro Lopez 65’, Jimmy Briand 76’)
Stadion Maksimir, Zagreb
Qualifiers for Round of 16
Group A - Bayern Munich, Napoli
Group B - Inter Milan, CSKA Moscow
Group C - Benfica, FC Basel
Group D - Real Madrid, Lyon
Group E - Chelsea, Bayer Leverkusen
Group F - Arsenal, Marseille
Group G - APOEL Nicosia, Zenit St Petersburg
Group H - Barcelona, AC Milan