Two-time defending champions Sevilla survived on penalties, seeing off Spanish rivals Athletic Bilboa 5-4 in a shootout after Athletic won the second leg 2-1 and the tie ended 3-3 on aggregate.
Kevin Gameiro scored the final penalty despite pulling up injured in the final minute of extra time as Sevilla made it through.
There were no goals in the first half, though Aritz Aduriz hit the outside of the post from a tight angle and Adil Rami somehow put the ball over the bar from close range.
Aduriz did find the net in the 57th minute when he cut into the centre before beating David Soria at his near post.
But the lead only lasted two minutes as Gameiro tapped in Grzegorz Krychowiak's cross for Sevilla.
Aduriz was forced off with an injury in the 70th minute as Athletic pushed forward to try to force extra time, but Raul Garcia was able to find the all-important goal with a looping header 10 minutes later.
Neither team could find the edge in the extra 30 minutes, though Gameiro pulled up limping and stayed down for treatment in the 120th minute.
But he recovered enough to take the fifth penalty after Athletic's Benat saw his shot saved in the fourth round of spot-kicks.
Coke, Krychowiak, Yevhen Konoplyanka, and Steven N'Zonzi also successfully converted for Sevilla, while Raul Garcia, Borja Viguera, Mikel San Jose and Markel Susaeta were on target for the visitors.
Cedric Bakambu scored twice as Villarreal glided to a 4-2 win at Sparta Prague to advance 6-3 on aggregate.
Bakambu dashed the hosts' hopes in only the fifth minute as he raced onto Manu Trigueros' fine through ball and shook off the attentions of a defender before slotting home.
Samu Castillejo added a second two minutes before the break when he controlled a Denis Suarez cross and had time to pick his spot before shooting into the corner.
And in first-half stoppage time Bruno put the game to bed with a header following Castillejo's corner.
Bakambu added his second and Villarreal's fourth in the 49th minute after bringing down Suarez's cross in the centre of the box.
Sparta found consolation goals through Borek Dockal and Ladislav Krejcl, but the damage had already been done.
Ricardo Ferreira was responsible for two own goals as Shakhtar Donetsk cruised to a 4-0 victory at home over Braga to wrap up a 6-1 aggregate win.
Braga keeper Matheus brought down Viktor Kovalenko in the box and Darijo Srna converted the resulting penalty for the opener in the 25th minute.
It was 2-0 in the 42nd minute when Matheus misplayed a cross which fell to the far post where it bounced in off Ferreira.
Kovalenko added a third goal five minutes after the break by turning in a pass from Srna, and Ferreira was again unlucky on 74 minutes
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