Reigning UEFA Europa League champions Atletico Madrid suffered a shock 2-0 defeat to Group B rivals Academica in Portugal.
Guaranteed
Rubin Kazan and Inter Milan booked their respective places in the knock-out stages after securing victories which guaranteed their progress from Group H.
Vladimir Dyadyun's 19th-minute goal gave the Russians a 1-0 win at Neftchi while two second-half strikes from substitute Rodrigo Palacio helped Inter end Partizan's hopes with a 3-1 triumph in Belgrade.
Fredy Guarin also scored for the visitors, while Nemanja Tomic replied for Partizan in injury-time. The group winners are likely to be determined when Rubin face Inter in Russia in a fortnight's time.
Lyon maintained their 100 per cent record and ensured qualification from Group I after beating last year's runners-up Athletic Bilbao 3-2 in Spain.
Bafetimbi Gomis and Yoann Gourcuff put the visitors 2-0 up at the break and despite Ander Herrera and Aritz Aduriz pulling Bilbao level, Alexandre Lacazette grabbed a 63rd-minute winner.
Also in Group I, Sparta Prague all but assured qualification after a 1-1 draw with Ironi Kiryat Shmona in Israel, Leonard Kweuke cancelling out Darko Tasevski's early goal for the hosts.
Two Libor Kozak goals kept Lazio on top of Group J with a 3-0 win over Panathinaikos at the Stadio Olimpico. Sergio Floccari added a 59t- minute third for Vladimir Petkovic's men.
Also in Group J, a Jermain Defoe hat-trick helped Tottenham take a big stride towards qualification with a 3-1 win over Maribor at White Hart Lane. Robert Beric briefly equalised for the visitors.
Ukrainians Metalist Kharkiv confirmed their progress from Group K with a 3-1 win over Rosenborg. Taison, Cleiton Xavier and Juan Manuel Torres scored for the hosts with Borek Dockal replying for the Norwegians.
And Bayer Leverkusen will join Metalist in the knockout stages after coasting to a 3-0 win over Rapid Vienna with goals from Jens Hegeler, Andre Schurrle and Manuel Friedrich.
Hannover booked their passage from Group L after a dramatic 3-2 win over Helsingborg, who finished with nine men.
A double from Mame Biram Diouf gave the Germans a comfortable advantage before Nikola Djurdjic and Alejandro Bedoya dragged the score back level.
But the Swedes had Peter Larsson and Walid Atta both sent off in the closing minutes before Szabolcs Huszti struck the winner with an injury-time penalty. Meanwhile, group rivals Twente and Levante drew 0-0 in Holland.
Marco Streller scored an 80th-minute winner as Basle kept their Group G hopes alive with a 1-0 win over Videoton, while group leaders Genk needed an injury-time equaliser from Glynor Plet to rescue a 1-1 draw at Sporting Lisbon, who despite being down to 10 men due to the dismissal of Stijn Schaars had led through a Ricky van Wolfswinkel goal.
