The Spanish side won 5-0 in the second leg at Wroclaw's Municipal Stadium with Carlos Bacca scoring twice. Ivan Rakitic, Jairo Samperio and Diego Perotti also got on the scoresheet.
Remarkably, Wroclaw could still join them in the next phase as all losing teams are to be placed into a random draw to replace the expelled Fenerbahce.
Dynamo Kiev were also convincing winners, beating Kazakh club Aktobe 5-1 for an 8-3 aggregate success.
Jeremain Lens, Roman Bezus, Dieumerci Mbokani, Ideye Brown - with a penalty - and captain Oleh Gusev struck as the Ukrainian side turned on the style after a close first leg.
Turkish side Besiktas overturned a first-leg deficit to see off Tromso 3-2 on aggregate with a 2-0 win in Istanbul. Hugo Almeida and Oguzhan Ozyakup both struck in the space two minutes early in the second half.
Rapid Vienna struck three times without reply in Tblisi to end any hopes Georgian side Dila Gori may have had of causing an upset.
Gori trailed just 1-0 after the first leg in Austria but their hopes of overturning that on home soil ended as Louis Schaub put Rapid in command in first-half injury time and Marcel Sabitzer and Brian Behrendt completed the job.
Dutch side Feyenoord were unable to turn around their tie against Russians Kuban Krasnodar despite a bright start in Rotterdam, losing 2-1 to go out 3-1 on aggregate.
Graziano Pelle had a fourth-minute penalty saved but made amends by scoring three minutes later to level the tie for Feyenoord at 1-1. The momentum could not be maintained though and Kuban went through after goals from Ivelin Popov and Gheorghe Bucur.
Fiorentina needed to rely on away goals to oust Swiss side Grasshoppers after losing their second leg 1-0 in Florence. Nassim Ben Khalifa put the Zurich team in the ascendancy but the Italians' first-leg efforts proved decisive after a 2-2 aggregate draw.
A goal by Goran Mujanovic in the fourth minute of injury time sent Croatian side Rijeka through at the expense of Stuttgart, 4-3 on aggregate.
Extra time was looming with the Germans leading 2-1 on the night, courtesy of a Christian Gentner effort and a Luka Maric own goal. Rijeka had earlier scored through Leon Benko.
Slovan Liberec held off Udinese to progress 4-2 after a 1-1 draw in the Czech Republic. Dzon Delarge put Liberec in sight of the group stage before Andrea Lazzari pulled one back.
Swiss club St Gallen produced a superb performance to crush Spartak Moscow 4-2 in the Russian capital and progress 5-3 on aggregate.
Aras Ozbiliz gave Spartak an early lead but St Gallen hit back with two from Goran Karanovic and another from Roberto Rodriguez. Yura Movsisyan gave Spartak late hope but Dejan Janjatovic ended the scoring.
Real Betis were also in good goalscoring form, crushing Czechs Jablonec 6-0 to power through 8-1 overall.
Ruben Castro, Javier Matilla, Jorge Molina, Brian Rodriguez and Xavi Torres struck for Betis, who also benefited from a Vit Benes own goal.
Dutch side AZ Alkmaar and their Greek opponents Atromitos will need to return on Friday to play out the remaining 33 minutes of their second leg after a fire broke out at the AFAS Stadion.
Spectators were evacuated and play abandoned after 57 minutes with visitors leading 1-0, to trail 3-2 on aggregate.
The abandonment came just moments after Dimitris Papadopoulos had scored to give the Greeks further hope after the Dutch side had Markus Henriksen sent off in the early stages.