Everton were among the first teams to be eliminated from the Europa League group stage after losing 3-0 to Lyon on Thursday.
Managerless Everton's recent woes continued as Cuco Martina was taken off on a stretcher with an unspecified injury minutes before half-time.
Bertrand Traore then scored on a second-half counter-attack and Houssem Aouar added a second for the French side, while Everton's hopes of a comeback ended when Morgan Schneiderlin was sent off with a second booking in the 80th minute.
Former Manchester United winger Memphis Depay added a late third from a header to complete Lyon's win.
The Premier League club have only gained a single point from the four European games -- a draw with Apollon in September.
Lyon moved onto eight points, level with Group E leaders Atalanta, who were pegged back late in a 1-1 draw as Apollon's Emilio Zelaya equalised in the 94th minute.
Arsenal qualified for the knockout stage despite being held to a 0-0 home draw by Red Star Belgrade.
The Gunners had a good chance after 11 minutes when Ainsley Maitland-Niles found Olivier Giroud, whose strike was saved by Milan Borjan.
But home goalkeeper Matthew Macey had to tip a fine header from Vujadin Savic onto the crossbar and away and visiting striker Richmond Boakye shot wide with only the keeper to beat.
Boakye was again off target after the break, with Jack Wilshere coming closest for Arsenal when his effort was brilliantly cleared off the line by Damien Le Tallec.
Arsenal's qualification was confirmed as Cologne thrashed BATE Borisov 5-2 at home.
After Simon Zoller's opener for the Bundesliga club, BATE rallied to take a half-time lead, only for a Yuya Osako brace and goals from Sehrou Guirassy and Milos Jojic to turn the game back in the hosts' favour.
Arsenal need one more point to win the group after seeing their 100 percent record end, while Red Star are second with five points, one head of BATE and two ahead of Cologne.
In Group D, AC Milan were made to wait for confirmed qualification from the group stage after being held to a 0-0 draw in a mediocre game at AEK Athens.
Home defender Helder Lopes ventured forward to fire in the first meaningful strike of the game after 14 minutes, but Gianluigi Donnarumma made the save.
It took Milan 44 minutes to muster their first shot on goal of the game as Bonucci fired a wayward effort high and wide, and with almost an hour played they came within a whisker of opening the scoring as Montolivo thumped a fierce effort against the post.
Milan still top the group on eight points, two ahead of their opponents and four clear of Austria Vienna, who cruised to a 4-1 win away to Rijeka.
Two goals from Dominik Prokop sandwiched a Domagoj Pavicic effort for the hosts before Rijeka had Josip Misic sent off with 18 minutes remaining. Further goals from Tarkan Serbest and Christoph Monschein sealed the Austrians' win.
Marseille won 1-0 against Guimaraes in Portugal after defender Patrice Evra was sent off before the start of the game following a heated confrontation with a supporter.
Christopher Hurtado scored the only goal after 80 minutes before Marseille also had Boubacar Kamara sent off. Meanwhile, Salzburg still top Group I after a goalless draw with Konyaspor.
Lazio sealed qualification from Group K after a last minute own goal from Maxime Le Marchand gave them a 1-0 win over Nice, while goals from Marvin Baudry and Onur Kaya gave Zulte-Waregem a 2-0 win at Vitesse, where Zulte's Kingsley Madu and Vitesse's Alexander Buttner were sent off.
Dynamo Kiev made it through to the knockout stage by defeating Young Boys 1-0 in Group B.
Vitaliy Buyalskiy's 70th-minute goal in Bern kept Dynamo atop Group B, two points above Partizan Belgrade, who are second after beating Skenderbeu 2-0 with goals from Zoran Tosic and Leandre Kana.
Zenit St.Petersburg effectively sealed their passage from Group L with a 1-1 draw away to Rosenborg, Aleksandr Kokorin salvaging a point with the last kick after Nicklas Bendtner's penalty put the hosts ahead.
Real Sociedad are also firmly on course for the knockout stages, Alberto De La Bella's volley the pick of their goals in a 3-0 win over Vardar.
Villarreal stayed top of Group A with a 2-0 win at Slavia Prague, Carlos Bacca hitting an early opener and Simon Deli scoring an own goal two minutes from time.
Astana moved above Slavia into the second qualifying slot with a 1-0 win at Maccabi Tel Aviv, who were eliminated after Patrick Twumasi scored the only goal on 57 minutes.
Steaua Bucharest are through to the next round from Group G after a 1-1 draw with Hapoel Be'er Sheva. Florinel Coman put Steaua ahead on 31 minutes but Ben Sahar equalised.
Viktoria Plzen moved clear in second with a 4-1 win over Lugano with a brace from Michal Krmencik.
The bottom two clubs both won in Group J, Aritz Aduriz giving Athletic Bilbao a 1-0 win over Ostersunds despite the sending-off of Unai Nunez while Hertha Berlin beat Zorya 2-0 with a Davie Seike double. Ostersunds still lead the group but Bilbao are now just two points behind.
There was no change in Group C as leaders Ludogorets were held to a 1-1 draw by second-placed Braga, Marcelinho's opener cancelled out by another Brazilian, Fransergio, for Braga seven minutes from time.
Third-placed Hoffenheim failed to capitalise as Edin Visca hit an injury time equaliser for hosts Istanbul Basaksehir, after Florian Grillitsch's early second half strike had put the hosts in command.
Lokomotiv Moscow crashed from first to third in Group F after a shock 2-1 home defeat to Sheriff. The hosts led through Jefferson Farfan but Ziguy Badibanga and Josip Brezovec replied for the visitors.
FC Copenhagen joined Sheriff on top of the group after a 3-0 win over Zlin with goals from Michael Luftner and a brace from Benjamin Verbic.