Cristiano Ronaldo had opened the scoring early on but Aaron Wan Bissaka’s red card then reversed the Red Devil’s momentum.
The Swiss champions got an equalizer through Cameroonian winger Nicolas Ngamaleu on 66 minutes, before Jordan Siebatcheu scored the winner in extra time.
In London, Chelsea registered an important 1-0 win against Zenit St Petersburg. Zenit had spent the vast majority of the half defending with all eleven players in their defensive third.
But the hosts’ pressure paid off in the 69th minute when Romelu Lukaku headed home an Azpilicueta cross.
Sevilla 1-1 RB Salzburg
Lille 0-0 Wolfsburg
Barcelona 0-3 Bayern
Villareal 2-2 Atalanta
Malmo 0-3 Juventus
Dynamo Kyiv 0-0 Benfica