Red Star, which won the European Cup in 1991, advanced on the away goals rule after winning the first leg 1-0 at home.
Steaua Bucharest, another former European Cup champion, also advanced thanks to a 2-1 victory over Poland's Zaglebie Lubin and 3-1 aggregate win.
The biggest upset was the elimination of Belgium's Racing Genk, which won, 1-0, at Bosnia's Sarajevo but couldn't make up its 2-1 loss at home.
The biggest margin of victory was Rosenborg's 7-1 win over Kazakhstan champion Astana -- Ivory Coast's Abdoulrazak Traore scored a hat trick -- to send the Norwegian team through with a 10-2 aggregate victory.
Rich Ukrainian club Shakhtar Donetsk, which recently bought Mexican star Nery Castillo, got a scare from Pyunik of Armenia before winning, 2-1, and advancing to the third round, 4-1, on aggregate.
Oleksandr Gladkiy, another recent signing, and Brandao scored in both legs for Donetsk.