Marseille were stunned 1-0 by Slovan Liberec, who claimed victory at the Stade Velodrome thanks to Vladimir Coufal's goal six minutes from time. Sporting Braga are now top of Group F thanks to a 1-0 defeat of Groningen.
It was a disappointing night for French sides, with Saint-Etienne losing 3-2 at Lazio in a frenetic Group G encounter that saw Robert Beric and Moustapha Bayal Sall sent off for the visitors. Dnipro won 1-0 at Rosenborg in the other match in the group.
Group D leaders Napoli won 2-0 at Legia Warsaw and Midtjylland made it two wins from two with a 3-1 victory at Club Brugge.
Fiorentina eased to a 4-0 away triumph over Belenenses in Group I and Basel beat 10-man Lech Poznan 2-0. Franco Di Santo scored a hat-trick as Schalke defeated Group K rivals Asteras Tripolis 4-0, and Sparta Prague overcame APOEL 2-0.
AZ defeated Athletic Bilbao 2-1 in a Group L match, while Partizan won 3-1 at Augsburg despite seeing Aleksandar Subic sent off.
In Group E Villarreal beat 10-man Viktoria Plzen 1-0 and Rapid Vienna overcame Dinamo Minsk by the same scoreline. Group H saw Lokomotiv Moscow defeat Skenderbeu Korce 2-0 and Besiktas draw 1-1 with Sporting Lisbon.