Europa League holders Atletico Madrid and Viktoria Plzen both ensured qualification from Group B with the group winners to be decided when the two teams clash in the Czech Republic next month.
Raul Garcia's seventh-minute strike proved enough for Atletico to defeat Hapoel Tel Aviv in Spain, while Plzen drew 1-1 with Academica in Portugal, Pavel Horvath's penalty cancelled out by a late Edinho spot-kick for the hosts.
Fenerbahce went through as Group C winners with Bekir Irtegun scoring the only goal of the game against Marseille at the Stade Velodrome, while Borussia Monchengladbach beat Cypriots AEL 2-0 to go through with them.
Substitute Igor de Camargo scored twice in the last 10 minutes for Monchengladbach after the visitors had Luciano Bebe sent off. The win leaves the Germans three points ahead of Marseille and with a better head-to-head record.
Jose Salomon Rondon scored twice in the last three minutes as Rubin Kazan booked top spot in Group H with a 3-0 win over Inter Milan.
The Italians named an inexperienced line-up for a game between two sides who had already reached the knockout stages, and it showed as Gokdeniz Karadeniz struck in the opening minute and substitute Rondon added his late brace.
Also in Group H, Aleksandar Mitrovic scored and was later sent off as Partizan Belgrade came back from behind to draw 1-1 away to Neftchi, for whom Venancio Flavinho opened the scoring early on.
Group G leaders Genk sealed their place in the knockout stages with Elyaniv Barda's 19th-minute goal enough to see off Videoton in Hungary.
Swiss side Basle moved two points clear in second place as they shrugged off the 59th-minute dismissal of midfielder Cabral to beat Sporting Lisbon 3-0 with goals from Fabian Schar, Valentin Stocker and David Degen.
Sporting, last season's semi-finalists, are now out of contention for a last-32 berth.
Lyon lost the last remaining 100 per cent record but confirmed top spot in Group I with a 1-1 draw against Sparta Prague in the Czech Republic. Teenager Yassine Benzia gave the French side a 46th-minute lead and Josef Husbauer replied seven minutes later.
The point is also enough for the Czechs to progress at the expense of Hapoel Kiryat Shmona and last year's runners-up Athletic Bilbao, whose match in Israel was postponed due to safety fears.
Tournament debutants Levante confirmed qualification from Group L, the Spaniards advancing with a 3-1 win at Helsingborgs with goals from Angel, Pape Diop and Vicente Iborra, before Thomas Sorum hit a late consolation for the hosts.
Already-qualified Hannover, meanwhile, were held to a goalless home draw by FC Twente, who had Rasmus Bengtsson sent off late on. The group winners will be determined when Levante and Hannover clash in Spain next month.
Jonathan Cristaldo and Cleiton Xavier scored in the second half to confirm Metalist Kharkiv as winners of Group K after a 2-0 win over Bayer Leverkusen, who had also already qualified.
Also in Group K, Rosenborg hit back to beat Rapid Vienna 3-2. John Chibuike put the hosts ahead before the Austrians hit back through Thomas Schrammel and Terrence Boyd. Rosenborg won it in the last 10 minutes with goals from Tarik Elyounoussi and Rade Prica.
Lazio's goalless draw with Tottenham in Group J was enough to send the Italians through but second place remains far from certain after a Victor Vitolo penalty gave Panathinaikos a 1-0 win over Maribor, who had Ales Mejac sent off.
The result means Spurs and Panathinaikos will effectively play off for second place at White Hart Lane next month, with anything other than a defeat good enough for the Londoners.
Second half goals from Christopher Samba and Samuel Eto'o booked Anzhi Makhachkala's qualification from Group A with a 2-0 win over Udinese in Russia.
Bordeaux joined Newcastle in qualification from Group D and will effectively play off for the status of group winners in France next month.
Two goals from Jussie gave Bordeaux a 2-1 win at Club Brugge, for whom Maxime Lestienne replied.
Shinji Okazaki scored twice as Stuttgart blew Group E wide open with a stunning 5-1 win away to leaders Steaua Bucharest. Serdar Tasci, Martin Harnik and Gotuko Sakai also scored for the Germans before Mihai Costa replied.
Neither side are guaranteed progress to the knockout stages after Copenhagen's 2-1 win at Molde. Cesar Santin put the Danes ahead from the spot and after Daniel Chukwa's equaliser, Rurik Gislason scored a 76th-minute winner.
Copenhagen face Steaua at home in their final group game next month knowing a win could be enough to send them through at the expense of either the Romanians or the Germans.
Edison Cavani's injury-time penalty sent 10-man Napoli through from Group F with a 2-1 win over AIK in Sweden.
Blerim Dzemaili put the Italians ahead but Helgi Danielsson's equaliser looked set to keep the group wide open until Cavani struck from the spot shortly after Salvatore Aronica had been sent off.
Group leaders Dnipro also sealed their passage with a 2-1 win at PSV. Georgino Wijnaldum put PSV ahead but Dnipro replied through Yevhen Seleznyov and Yevhen Konoplyanka, before Jaba Kankava was sent off late.