After trailing 1-0 after the opening tie, Russian side Zenit claimed a 3-0 win at Stadion Petrovskij thanks to goals by Jose Salomon Rondon, Danny and Alexander Kerzhakov.
Meanwhile, Celtic's hopes of another European campaign were ended as they were beaten 2-0 by Legia Warsaw, meaning they lost 6-1 on aggregate. Michal Zyro and Michal Kucharczyk scored for the Polish side to wrap up a comprehensive victory over two legs.
Anders Jacobson scored twice as Danish side Aalborg came through 2-0 to defeat Dinamo Zagreb 2-1 on aggregate, while Martin Hinteregger's double saw Salzburg claim a 2-0 second leg victory as his side progressed 3-2 overall winners against Azerbaijan side Qarabag Agdam.
Elsewhere, APOEL defeated HJK 2-0 for a 4-2 aggregate win, while Slovan Bratislava progress despite a goalless draw against Sheriff thanks to their 2-1 win in the opening clash, Malmo progressed on away goals against Sparta Prague and Besiktas took a 5-2 aggregate win over Feyenoord thanks to a 3-1 win on Wednesday.
Steaua Bucharest and FC Copenhagen also progressed, as did Ludogorets on away goals thanks to Marcelinho's double after they drew 2-2 against Partizan Belgrade following a goalless opening encounter.