Sevilla - who beat Benfica in the final last term - left it late to secure their passage to the knockout stages, entering matchday six with their spot in the balance.
But a 1-0 Group G win over Croatia's Rijeka did the job - Denis Suarez scoring the 20th-minute winner for Unai Emery's men.
Feyenoord, who had already qualified, thrashed Standard Liege 3-0 in the other pool match.
Azerbaijan's Qarabag - in the Europa League group stage for the first time - started Thursday second in Group F, but slipped out after a dramatic finale against Inter.
Richard Almeida thought he had sent Qarabag into the last 32 when his 93rd-minute strike was deflected in off Inter defender Isaac Donkor.
The joyous scenes in Baku were cut short, though, with Leroy George adjudged to be offside - giving Dnipro Dnipropetrovsk a lifeline they held onto after beating Saint-Etienne 1-0 in Group F's other game.
Inter had already secured qualification and the pool win, with Dnipro now joining them in the last 32.
Ricardo Rodriguez scored twice as a 10-man Wolfsburg won 3-0 at Lille to secure their progression. The other Group H match saw Everton, already guaranteed to finish first, lose 1-0 at home to Krasnodar after fielding a weakened team.
Branimir Hrgota scored twice as Borussia Monchengladbach beat FC Zurich 3-0 to win Group A, while Villarreal finished second after a 2-0 triumph at Apollon in Cyprus .
Two separate floodlight failures interrupted Besiktas' 1-0 win over Tottenham, a result that saw the Turkish side finish on top of Group C at the visitors' expense. Partizan Belgrade and Asteras Tripolis played out a goalless stalemate in the same pool.
Club Brugge needed an 88th-minute goal from Lior Refealov to beat HJK Helsinki 2-1 in Group B, a result that saw them top the pool. Torino also went through after thrashing FC Copenhagen 5-1.
Young Boys moved into the last 32 at the expense of Sparta Prague with a 2-0 win, while Group I winners Napoli eased past Slovan Bratislava 3-0.
Steaua Bucharest were eliminated after losing 2-0 at home to Dinamo Kiev, who won Group J. A win would have been enough for the Romanians after bottom-placed Rio Ave surprised AaB 2-0.
Celtic had already qualified but lost 4-3 against a Marko Pjaca-inspired Dinamo Zagreb. Pjaca scored a hat-trick as Dinamo moved off bottom in Group D - going ahead of Astra, who lost 5-1 to pool winners Salzburg.
Guingamp and Dinamo Minsk posted 2-1 away wins in Group K at PAOK and Fiorentina respectively. Guingamp's win was enough for them to finish second, three points behind the Serie A side.
The Group E picture was settled prior to kick off - Dinamo Moscow as winners and PSV in second. Dinamo beat the Dutch side 1-0, while already eliminated Panathinaikos and Estoril drew 1-1.
Legia Warsaw made it five wins from six Group L matches with a 2-0 success against the team to join them in the last 32, Trabzonspor. Lokeren triumphed 1-0 at Metalist, leaving the losers without a point from the group stage.
The 24 sides that qualified from the 12 Europa League groups will be joined in the knockout rounds by Olympiacos, Zenit, Sporting, Athletic Bilbao, Liverpool, Anderlecht, Roma and Ajax.
The eight sides dropped into Europe's second-tier competition after finishing third in their respective UEFA Champions League groups.
