Marseille advanced from Group I after a 0-0 home draw to group winner Salzburg. Bilbao clinched the top spot in Group J after a 2-0 victory at Ukraine's Zorya Luhansk. In the battle for second spot in Group H behind already-qualified Arsenal, Red Star Belgrade eliminated Cologne with a 1-0 victory.
Earlier, Copenhagen and Lokomotiv both advanced from the tightly contested Group F after victories over Sheriff Tiraspol and Zlin, respectively. AEK needed a point and got it from a 0-0 draw at Austria Vienna to join AC Milan in the next phase from Group D.
Two other clubs advanced from the early kickoffs, with Astana making it through from Group A after a 1-0 victory at Slavia Prague, and a 1-1 draw at Hoffenheim proving enough for Bulgaria's Ludogorets Razgrad to qualify from Group C.
Sixteen clubs had already booked their places in the round of 32, which will also include eight third-place teams from the group stage of the Champions League. Elsewhere, already eliminated Everton recorded its first victory of the campaign, a 3-0 win at Apollon Limassol, courtesy of two first-half strikes by Ademola Lookman and another by Nikola Vlasic three minutes before the final whistle.
The draw for the Round of 32 will be held on Monday. Here's a look at Thursday's Europa League action:
Croatian champion Rijeka spoiled the European debut for Milan's new coach Gennaro Gattuso with a 2-0 victory in Group D.
A perfectly executed free kick by Jakov Puljic shocked the Italian powerhouse seven minutes into the game and Mario Gavranovic extended that lead two minutes into the second half.
Milan, one of the competition's favorites, had already secured top spot in the group with 11 points, three more than AEK, which drew its last five group stage games.
Rijeka and Austria Vienna are eliminated.
Pieros Sotiriou and Michael Lueftner scored in the space of three minutes early in the second half to help Copenhagen to a 2-0 victory over Sheriff Tiraspol and a place in the next stage. Group F had remained wide open until the last round of matches.
A draw would have been enough for the Moldovan champions to make the next round for the first time.
Aleksei Miranchuk scored in the 70th minute and Jefferson Farfan added another five minutes later for Lokomotiv to seal a 2-0 away victory over Czech side Zlin.
Lokomotiv finished top of the group with 11 points, followed by Copenhagen two points behind. Tiraspol also finished on nine points but was eliminated by its head-to-head results.
EASY FOR ARSENAL
Already certain to finish top of Group H, Arsenal completed the group stage with 13 points and a 6-0 rout of BATE Borisov.
Mathieu Debuchy, Theo Walcott and Jack Wilshere all scored in the first half to put the outcome beyond doubt. Denis Polyakov made it 4-0 in the second half with an own goal before Olivier Giroud netted from the penalty spot for his 17th goal in his 40th appearance in European competitions. Mohamed Elneny finished BATE off with the sixth.
Cologne has endured a miserable season at home after 11 losses in 14 games, and has only three points at the bottom of the Bundesliga.
Europe is no consolation.
Midfielder Slavoljub Srnic scored the decider in the 22nd minute for Red Star to join Arsenal in the next round with nine points.
Cologne is eliminated with six points, followed by Borisov on five.