Arsenal qualified despite dropping their first points in Group H as they were held 0-0 at home by Red Star Belgrade while Lazio, Dynamo Kiev and FCSB, formerly Steaua Bucharest, joined them in the round of 32.
There was an extraordinary start at Vitoria Guimaraes where visitors Olympique Marseille had substitute Patrice Evra sent off before kick-off after players became involved in a brawl with fans of their own team.
An Olympique player identified by the media as Evra was seen aiming a karate-style kick at supporters who had invaded the area behind the goal.
Vitoria completed Olympique's misery by winning 1-0 with a late goal and the French side had Boubacar Kamara sent off for a second yellow card offence.
Olympique Lyon scored three times in the last 25 minutes to leave Everton bottom of Group E with one point and end their hopes of progressing with two games left.
Bertrand Traore put Lyon ahead in the 68th minute as he sped past Ashley Williams and steered the ball past goalkeeper Jordan Pickford.
Houssem Aouar turned in the second from Memphis Depay's pass and Depay headed the third in the 90th minute. To add to the indignity, Everton had Morgan Schneiderlin sent off for a second bookable offence 10 minutes from the end.
Lyon joined Atalanta on eight points at the top of the group after the Serie A side conceded a last-minute goal and were held 1-1 at Apollon in Cyprus.
Milan stayed top of Group D with 8 points, two ahead of their Greek rivals, although they really needed a win to lift the pressure on coach Vincenzo Montella.
Riccardo Montolivo hit the post for the Italians early in the second half and that was as close as they got.
Dinamo Kiev went through with a 1-0 win at Young Boys as Vitaliy Buyalskiy scored the winner in their Group B match.
Lazio are the only team with 12 points from their four games after a stoppage-time own goal by Maximie Le Marchand, who turned a corner into his own net, gave them a 1-0 win at home to Nice in Group K.
FCSB qualified from Group G despite dropping their first points in a 1-1 draw at home to Hapoel Beer Sheva.
Carlos Bacca and a Simon Deli own goal gave Villarreal a 2-0 win at Slavia Prague which took them top of Group A with eight points.
Moldova's Sheriff Tiraspol pulled off a shock 2-1 win at Lokomotiv Moscow to go level on six points with FC Copenhagen at the top of Group F.
Table-propping Bundesliga side FC Cologne, winless in the league after 10 matches, hammered BATE Borisov 5-2, scoring more goals than they have managed all season domestically.
(Writing by Brian Homewood in Berne; Editing by Ed Osmond)
