Bordeaux lost their 100% record in the tournament as a last-minute goal saw them defeated 2-1 in Anderlecht.
Mbo Mpenza scored the injury-time winner as the Belgians came from behind after Jan Polak equalised Ferreira Jussie’s opener.
Marseille put one foot in the last 16 with three second half goals from Benoit Cheyrou, Taye Taiwo and Mamadou Niang at home to Spartak Moscow.
Braga were made to pay for two missed penalties as Werder Bremen hit three unanswered goals at the Weserstadion.
Naldo, Daniel Jensen and Hugo Almeida were all on the scoresheet as goalkeeper Tim Wiese saved spot-kicks from Roland Linz and Jorginho.
PSV Eindhoven beat Helsingborg 2-0 thanks to goals from Timmy Simons and Danko Lazovic.
Simon Vukcevic scored both goals as Sporting Lisbon beat Basle, while Pavel Pogrebniak’s 63rd-minute strike gave Zenit St Petersburg a narrow 1-0 win against Villarreal in Russia.
Getafe drew 1-1 at AEK Athens with goals from the Spaniard’s Ruben de la Red and Ismael Blanco coming in the last four minutes, while Galatasaray’s match at home to Bayer Leverkusen finished goalless.