Matias Emilio Delgado scored in the 56th and 64th minutes for Besiktas in a 2-0 win over FC Zurich. Besiktas reached the group stage for the first time in four seasons with the 3-1 aggregate win.
Another Istanbul club, Fenerbahce also advanced with a 2-0 win at Anderlecht in a match that was briefly interrupted by rowdy fans.
Mateja Kezman scored the first goal in the third minute and Alex de Souza added the other in the 77th minute.
Referee Massimo Busacca halted the match for five minutes in the 81st minute after about 50 Anderlecht supporters tried to push through a barricade to enter the field. Riot police also had to keep Fenerbache and Anderlecht fans apart after bottles and garbage was thrown between the two camps.
Valencia beat Swedish champions Elfsborg 2-1 to advance on a 5-1 aggregate.
Ivan Helguera gave the Spanish side a 1-0 lead in the fourth minute. Daniel Alexandersson equalized in the 31st minute, before Daniel Vila's winner in the 90th minute.
Benfica, champions in 1961 and 1962, beat FC Copenhagen 1-0 on Kostas Katsouranis's 18th minute goal and advanced 3-1 on aggregate.
Norway's Rosenborg advanced 5-0 on aggregate with a 2-0 win over Tampere United of Finland, with goals from Marek Sapara and Didier Konan Ya. The match was delayed by almost one hour because of a power failure at the Lerkendal Stadium.
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