Lyon booked their path to the next phase after a 4-2 aggregate victory over Rubin Kazan. Having won the first meeting 3-1, Lyon snatched a 1-1 draw in Russia as Bakary Kone cancelled out Bebras Natcho's goal.
Benfica put in an impressive performance at home to FC Twente, recording a 3-1 triumph that saw them progress.
Axel Witsel fired in a second-half brace before skipper Luisao added to the scoreline. Bryan Ruiz netted a consolation for FC Twente, as the tie finished 5-3 on aggregate in favour of the Portuguese club.
Belarusian side FC BATE Borisov are also through following a 2-0 victory over Sturm Graz via goals from Aleksandr Volodko and Marko Simic, the tie ending 3-1 on aggregate after a 1-1 draw in the first leg.
FC Viktoria Plzen added their name to the hat with a 2-1 (5-2 on aggregate) scalp of Copenhagen, who went in front on Wednesday night courtesy of Christian Bolanos' strike.
But any hope of a comeback was extinguished when Marek Bakos and Michal Duris both scored for the home side in the second period.