Ireneusz Jellen bagged a first half brace for the Ligue 1 outfit with Lionel Mathis sealing the win after Eduardo da Silva had given the visitors slight hope of a comeback just after the hour mark.
Elsewhere, Erwin Koeman's Feyenoord scraped through on away goals after a goalless draw against Lokomotiv Sofia in Rotterdam.
The Dutch side had scored two vital away goals in the first leg a fortnight ago, and they proved crucial as Loko failed to find the back of the net this time round.
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Besitkas scored twice in extra time to seal their passage into the group stage with a 2-2 draw against CSKA Sofia in Bulgaria.
The Turkish side headed into the tie two goals to the good after winning a fortnight ago in Istanbul, but CSKA fought back with second half goals from Iliev and Tunchev to send the match into an additional period of play.
But the Bulgarian fightback could not be sustained and goals from Brazilian strike duo Marcio Nobre and Devison Bobo saw the Turks through.
In other matches, Ajax had no problems in getting past Start, winning 8-2 on aggregate after a 3-0 win victory on the night. Fellow Dutch side AZ Alkmaar also progressed after a 1-1 draw with Kayserispor saw them through 4-3 over two legs.
Free scoring Dinamo Bucharest notched another four to defeat Xanthi 4-1 and book their place in the group stage with a 8-4 aggregate win whilst Lokommotiv Moscow were surprised by Belgian club Zulte Waregem, exiting the competition 3-2 on aggregate after falling to a 2-0 defeat on the night.
Crvena Zvezda also said goodbye to the tournament on Thursday as they slipped to a 2-1 defeat against Liberec in Belgrade. The Czech side went through 4-1 over the two legs, after having won 2-0 two weeks ago.
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