Lyon sealed their berth with a 2-0 aggregate win over their Zurich opponents, an 82nd-minute strike from Clement Grenier at the Letzigrund securing the French side a second 1-0 victory on Tuesday night.
They will join Arsenal as one of the seeded teams in the non-champions section of the draw.
Basel survived a major scare before booking their spot in the play-off stage at the expense of Maccabi Tel Aviv.
The Swiss club, last season's Europa League semi-finalists, had looked to be cruising through their third-round qualifying tie after netting three times in the opening 32 minutes through Fabian Schar (penalty), Mohamed Salah and Marcelo Diaz to extend their aggregate lead to 4-0.
However, hosts Maccabi hit back and an own goal from Schar (34) plus efforts from Eran Zahavi (37) and Maharan Radi (55) saw the Israeli side draw level at 3-3 on the night.
Maccabi could not find any more goals though and Swiss champions Basel held on to progress through.
Fenerbahce, who started the summer with a two-year suspension from European competition for alleged involvement in match-fixing before having that ban suspended by the Court of Arbitration for Sport, are also through after beating Red Bull Salzburg 4-2 on aggregate.
After earning a 1-1 draw from their trip to Austria, Fener completed the job on home soil on Tuesday night, although they needed to come from a goal down to do it.
Jonathan Soriano's fourth-minute effort put Salzburg ahead but the Turkish outfit scored three times in the next half-hour through Raul Meireles, Moussa Sow and Pierre Webo to take the win.
In Albania, visiting Shakhtyor Karagandy saw their 3-0 first-leg lead wiped out by Skenderbeu inside the opening 30 minutes, only for the Kazakh champions to recover and earn a 5-3 aggregate triumph.
Goals from Zeljko Tomic (nine) and Bledi Shkembi (20 and 29, both penalties) had Skenderbeu dreaming of a fairytale fightback, but Shakhtyor ended those hopes through goals from Sergey Khizhnichenko (38) and Maksat Baizhanov (67).
Bulgarian side Ludogorets' Champions League adventure continued as they knocked out Partizan Belgrade 3-1 on aggregate following a 1-0 win in Serbia. Hristo Zlatinski netted the only goal of the game from an 88th-minute penalty after Partizan defender Nikola Gulan had been sent off.
Steaua Bucharest, leading 2-0 from the first leg, won through against Dynamo Tbilisi following a 1-1 home draw. Iasmin Latovlevic's early goal extended Steaua's aggregate lead and Dynamo's only response was a 55th-minute goal from Ustaritz Aldekoaotalora.
Finally on Tuesday, a scoreless second leg in Slovenia was enough to send hosts Maribor through on away goals against Apoel Nicosia, the first leg having finished 1-1 in Cyprus.