Zenit St Petersburg claimed the final place as a seed for the Champions League playoff round non-champions draw after beating AEL 3-0 on Wednesday night.
Trailing 1-0 from the first leg, Zenit struggled to get back on level terms in tie before Jose Salomon Rondo finally found the back of the net 10 minutes after half-time. Andre Villas-Boas' side did not find the crucial goal to get their noses in front until the 88th minute when Danny scored.
Alexander Kerzhakov converted from the spot in the first minute of added time to end any hopes the Cypriot club had of causing an upset.
The result means Athetlic Bilbao face a tough task to qualify for the Champions League for the first time since 1998-99, as defeat for Zenit would have elevated the Spanish side into the seeds.
Besiktas secured a 5-2 aggregate win over Feyenoord thanks to a 3-1 win on Wednesday, with Demba Ba scoring a hat trick.
The draw for the final qualifying round takes place on Friday.
Seeded: Arsenal, FC Porto, Zenit St Petersburg, Bayer Leverkusen, Napoli
Unseeded: Athletic Bilbao, Lille, FC Copenhagen, Standard Liege, Besiktas.
There are several other ties on Wednesday night to decide the seeding for the champions route.
Celtic's humiliation was complete after they lost 2-0 at home to Legia Warsaw, resulting in a 6-1 aggregate loss.
Anders Jacobson scored twice as Danish side AaB came through 2-0 to defeat Dinamo Zagreb 2-1 on aggregate, while Martin Hinteregger's double saw Salzburg claim a 2-0 second leg victory as his side progressed 3-2 overall winners against Azerbaijan side Qarabag Agdam.
APOEL defeated HJK 2-0 for a 4-2 aggregate win, while Slovan Bratislava progress despite a goalless draw against Sheriff thanks to their 2-1 win in the opening clash, Malmo progressed on away goals against Sparta Prague.
Steaua Bucharest progressed, as did Ludogorets on away goals thanks to Marcelinho's double after they drew 2-2 against Partizan Belgrade following a goalless opening encounter.
The seeding for this half of the draw is as follows:
Seeded: FC Salzburg, Steaua Bucuresti, APOEL Nicosia, BATE Borisov, Ludogorets Razgrad
Unseeded: NK Maribor, Slovan Bratislava, Legia Warsaw, Malmo, AaB.