Holders Lyon, PSG set-up all-French Women’s Champions League semi-final
The victory set-up a last-four clash against French rivals Paris Saint-Germain who ended English hopes with a 2-1 win against Arsenal.
English international Nikita Parris gave six-time champions Lyon a 41st minute lead thanks to a pass from Eugenie Le Sommer.
Amel Majri added a second goal just before the hour off a curling free-kick.
Carolin Simon cut the deficit for Bayern on 64 minutes and was desperately unlucky when she hit the crossbar 15 minutes later.
Bayern may have failed to emulate their men’s team by reaching the Champions League final but PSG can still make it a double for the French capital.
Marie-Antoinette Katoto gave PSG a 15th-minute lead with a smart volley from a corner but Bethany Mead levelled for the Londoners, who were champions in 2007, six minutes before the break.
Young Danish star Signe Bruun hit the winner for the French side in the 77th minute with Katoto the provider.
On Friday, Denmark attacker Pernille Harder scored four goals as two-time winners Wolfsburg hammered Glasgow City 9-1 to reach the semi-finals.
In the other quarter-final, France’s Kheira Hamraoui claimed the match-winner to clinch a last four spot for last year’s runners-up Barcelona in a 1-0 win over Atletico Madrid.
Barca will face Wolfsburg in Tuesday’s other semi-final.