Holders Atletico Madrid were one of 13 sides to clinch their place in the last 32 of the Europa League after a 1-0 home win against Hapoel Tel Aviv.
Lazio qualified with a 0-0 draw against Tottenham, while Bordeaux joined Group D rivals Newcastle in the knockout stage after a 2-1 win at Club Bruges.
Anzhi Makhachkala progressed from Liverpool's Group A by beating Udinese.
Edinson Cavani's late winner clinched Napoli's 2-1 win at AIK and ensured they reached the knockout stage.
They were joined by Viktoria Plzen, Fenerbahce, Borussia Moenchengladbach, Dnipro Dnipropetrovsk, Sparta Prague, Levante and Genk.
Stuttgart won 5-1 at Steaua Bucharest, but must still overcome already-eliminated Molde in their final fixture to advance.
Diego Simone's Atletico Madrid, who beat Spanish rivals Athletic Bilbao in last season's final, only needed a draw against Israeli visitors Hapoel Tel Aviv to qualify from Group B and that was assured through Raul Garcia's seventh-minute strike.
Bilbao have been eliminated from Group I after Sparta Prague drew 1-1 against already-qualified visitors Lyon. The Basque side did not play after their match against Israeli hosts Hapoel Kiryat Shmona was postponed because of the security situation in the region.
French side Bordeaux knew they needed victory against Group D rivals Club Brugge and made the perfect start through Jussie's second-minute opener. The Brazilian forward doubled the lead shortly before the break as Maxime Lestienne's late strike proved irrelevant.
Two second-half goals in the space of four minutes, from ex-Blackburn defender Chris Samba and Cameroon superstar Samuel Eto'o, helped Russian side Anzhi Makhachkala win 2-0 against Udinese. It sealed their progress from Group A and eliminated the Italians.
Uruguay striker Cavani converted a 93rd-minute penalty as 10-man Napoli won 2-1 at Group F rivals AIK Solna. It meant the Swedish side were unable to wave a fond farewell in their final match at their Rasundastadion ground.
Stuttgart became the first team to score four first-half goals in a Europa League away tie as they ran riot at Group E leaders Steaua, while Group C front-runners Fenerbahce beat Joey Barton's Marseille.
Following Thursday's fixtures, there is one round of matches remaining before the competition enters the last-32 stage with the addition of eight teams dropping down from the Champions League.
Dynamo Kiev, Olympiakos and BATE Borisov are the only Champions League teams already confirmed as they are all guaranteed to finish third in their respective groups.