Braga, Metalist Kharkiv, Standard Liege and Hannover 96 were the other teams to go through to February's last 32.
Atletico Madrid, winners in 2010, won 1-0 at Celtic to qualify from Group I with one match to spare thanks to a powerful Arda Turan drive on the half-hour.
Ten-man PAOK qualified with a 2-1 win at Tottenham Hotspur, the Greeks all but eliminating last season's Champions League quarter-finalists with two early strikes.
Dimitris Salpingidis was gifted the opener after five minutes and Stefanos Athanasiadis added another eight minutes later after a sweeping move.
Luka Modric pulled one back for Tottenham in the 38th minute from a penalty harshly awarded for handball by Kostas Stafylidis, who was sent off, but PAOK held out after surviving a disallowed Jermain Defoe goal.
Rubin Kazan's 4-1 win over Shamrock Rovers, helped by two goals from Paraguay striker Nelson Haedo, sent the Russians three points clear of Tottenham with one match each to play and the pair level on their head-to-head record. However, Kazan have scored five more goals in Group A.
Metalist thrashed Austria Vienna 4-1 with Marko Devic, Edmar, Papa Gueye and Jose Ernesto Sosa sharing the goals for the Ukrainians who guaranteed top spot in Group G.
EXTRAORDINARY WIN
Braga's 1-0 win at home to English second tier side Birmingham City was enough for the 2011 runners-up in Group H, Hugo Viana scoring with a deflected shot after Nikola Zigic had missed an early penalty for the visitors.
Braga went through despite lying second behind group leaders Bruges, who are not yet certain of progression after their heroics in Slovenia where Ryan Donk scored at both ends in the Belgian team's extraordinary win.
Dalibor Volas gave Maribor an early lead which they doubled after half-time when Donk slid Dejan Trajkovski's low centre into his own net. Volas then stabbed home the third from close range in the 68th minute.
Moroccan Nabil Dirar scored twice in three minutes to start the fightback, Joseph Akpala equalised with eight minutes left and Donk headed the winner in the last minute.
There was still time for Volas to hit the post and miss out on a hat-trick in stoppage-time.
Standard Liege's 2-0 win over Hannover 96 in Group B sent both teams through after FC Copenhagen could only draw 1-1 at Vorskla Poltava.
Sporting, Anderlecht, PSV Eindhoven, Legia Warsaw, Twente Enschede and Athletic Bilbao had already qualified for the next round, where the third-placed teams from the Champions League groups enter Europe's second club competition.
