Four-time European Cup winner Ajax failed to advance to the Europa League last-32 after drawing 1-1 at home to Norwegian side Molde, as the nine remaining qualifying places for the knockout stage were decided on Thursday.
With so many places still available in the 12 groups, 20 teams were in contention before kickoff.
Ajax's hopes were raised when 18-year-old midfielder Donny van de Beek scored with a looping header in the 14th minute, but midfielder Harmeet Singh equalized for Molde in the 29th.
The Dutch side's draw handed the initiative back to Fenerbahce of Turkey, which went through in second - behind Molde - in Group A after drawing 1-1 with Celtic.
Former European Cup winner Marseille fared better, withstanding a late comeback to win 4-2 at Slovan Liberec and qualify ahead of the Czech side in Group F.
Midfielder Abdel Barrada set up first-half goals for Belgium striker Michy Batshuayi and winger Georges-Kevin N'koudou then scored an excellent third, chipping the ball over goalkeeper Tomas Koubek early into the second half.
The home side rallied as Marek Bakos and Josef Sural scored within a minute of each other, but Marseille substitute Lucas Ocampos rounded off a good night for the 1993 European champion when he coolly lobbed Koubek in injury time.
Senegalese striker Khouma Babacar grabbed the winner midway through the second half to send Italian side Fiorentina - a semifinalist last year - into the knockout stages with a 1-0 win against Belenenses of Portugal in Group I behind FC Basel.
In Group H, Algeria striker Islam Slimani scored his seventh goal in seven games as Sporting came from behind to beat Besiktas 3-1 and qualify at the expense of the Turkish side, which took the lead through Germany forward Mario Gomez in the 58th.
Lokomotiv Moscow joined Sporting in the next round as group winners after a convincing 3-0 win away to Albanian side Skenderbeu.
The remaining four places went to Swiss team Sion, Belgian side Anderlecht, Danish champion Midtjylland and Augsburg of Germany.
Sion went through after drawing 0-0 at home to Group B winner Liverpool, meaning that German coach Juergen Klopp's free-scoring Liverpool side has failed to find the net in two games.
Anderlecht qualified from Group J after beating Azerbaijan side Qarabag 2-1 at home, while Monaco's slim hopes ended with a crushing 4-1 defeat at group winner Tottenham - with midfielder Erik Lamela scoring a hat trick for the London side.
Midtjylland squeezed through behind Napoli in Group D with a 1-1 home draw against Club Brugge, which needed a win to overtake Midtjylland.
Augsburg rallied from conceding an early goal to score three second-half goals in a 3-1 win at Partizan.
With both teams finishing on nine points in Group L, Augusburg qualified ahead of the Serbian side.
Already qualified as Group D winner, Napoli rested top scorer Gonzalo Higuain, who has been in prolific form.
But there was little respite for Legia Warsaw as Dries Mertens struck twice in a 5-2 win in southern Italy.
Midfielders Nathaniel Chalobah, Lorenzo Insigne and Jose Callejon got the other goals to end Legia's hopes of qualifying.
With both sides already through, German side Schalke confirmed top spot in Group K ahead of Czech side Sparta Praha.
Schalke won 4-0 away to Greek side Asteras thanks to two goals from Cameroon forward Eric Choupo Moting, while Czech striker David Lafata also netted twice in Sparta's 3-1 win at APOEL Nicosia of Cyprus.