Reigning Europa League champions Atletico Madrid maintained their 100 per cent record in Group B with a 2-1 win over Academica.
Diego Costa and Emre Belozoglu put the Spanish outfit in control with strikes either side of half time before Salim Cisse hit a late consolation for the Portuguese side.
Also in Group B, Viktoria Plzen moved clear in second place with a 2-1 win at Hapoel Tel Aviv. Hanan Maman put the Israelis in front after 19 minutes, but Pavel Horvath equalised in first-half injury time and Frantisek Rajtoral hit the winner before home defender I'yad Hutba was sent off.
In Group A, Udinese suffered a shock 3-1 defeat away to bottom side Young Boys in Switzerland.
Raul Bobadilla grabbed a stunning hat-trick for Young Boys, who had gone into the game without a point, putting them 2-0 up with goals in the fourth and 72nd minutes and then wrapping up victory with a penalty after Andrea Coda had briefly reduced the deficit.
It was also all-change in Group C, where Egeman Korkmaz scored in the 72nd minute to give Fenerbahce a 1-0 win at AEL Limassol and move them to top the top of the group.
Marseille, who started the night on top, lost 2-0 at Borussia Monchengladbach, a Filip Daems penalty and a second-half strike from Peniel Mlapa moving the Germans level with their opponents on four points, with the Turkish side now out in front on seven.
Group D's second-placed side Bordeaux were held 1-1 at Maritimo as Yoan Gouffran's opener for the visitors was cancelled out by Roberge Valentin six minutes later.
Steaua Bucharest extended their lead at the top of Group E as goals from Vlad Chiriches and Raul Rusescu gave them a 2-0 win over Molde, while group rivals Stuttgart and FC Copenhagen played out a goalless draw in Germany.
Dnipro went five points clear at the top of Group F with an excellent 3-1 win over Napoli in Ukraine, Artem Fedetskiy, Matheus and Giuliano scoring before Edinson Cavani replied with a late consolation. PSV Eindhoven and AIK drew 1-1 in Holland, Kwame Karikari putting the previously pointless Swedes in front on the hour before Jeremain Lens equalised with 10 minutes to go.