Olympiakos dumped AC Milan out of the Europa League on Thursday after beating the seven-time European champions 3-1 in a pulsating clash in Greece, while Eintracht Frankfurt fans ran riot during the German side's win at Lazio and Celtic made the knockout stages despite losing to Salzburg at Celtic Park.
Captain Kostas Fortounis' penalty nine minutes from time saw the Greeks move into second place in Group F ahead of Gennaro Gattuso's Milan, who thought they had squeaked through when Cristian Zapata had pulled a goal back less than two minutes after putting the hosts 2-0 up with a comical own goal.
Olympiakos finished level on 10 points with Milan but qualified ahead of the Italians thanks to their superior goal difference following Milan's 3-1 win over the Greeks in October, and they end the group stage two points behind group winners Real Betis, who drew 0-0 at Dudelange.
Five Eintracht Frankfurt fans had been arrested in clashes with police in Rome ahead of their dead-rubber Group H match against Lazio as nearly 9,000 Germans swamped the Stadio Olimpico.
Eintracht had already comfortably taken top spot in the group thanks to winning all five of their previous games, while Lazio were also in the last 32 regardless of the result of the match, won 2-1 by the away side as they came back from a goal down thanks to second-half strikes from Mijat Gacinovic and Sebastien Haller.
However, German fans charged the pitch after Joaquin Correa's 56th-minute opener, and subsequently threw smoke bombs and flares at both Lazio fans and the police.
Last year's runners-up Marseille finished bottom of that group after losing 3-1 at home to Apollon Limassol and ending the group stage with just a single point.
Celtic looked to be following Old Firm rivals Rangers out of the competition after Steven Gerrard's side fell 1-0 at Rapid Vienna earlier on Thursday, but Tore Reginiussen's equaliser four minutes from time for Rosenborg at RB Leipzig allowed Brendan Rodgers's side to qualify second from Group B, two points ahead of the Bundesliga outfit.
Second-half goals from Munas Dabbur and Fredrik Gulbrandsen meant that Salzburg topped the group with a 100 percent record after a 2-1 win, while Olivier Ntcham's stoppage-time penalty meant nothing for the result nor the final standings.
Earlier Rangers, who had to win at Rapid Vienna in their final group game in order to qualify for the last 32, finished third in Group G after losing 1-0 to group winners Rapid, Dejan Ljubicic sealing the points in the 84th minute.
The Austrians are through to the knockout stages, level on 10 points with group winners Villarreal.
Slavia Prague ensured qualification ahead of Bordeaux by beating Group C winners Zenit St Petersburg 2-0, a result which made the French side's 1-0 win at FC Copenhagen irrelevant.
Chelsea, who had already won Group L, looked to be on their way to a perfect sixth win from six, but could only scrape a point at eliminated Vidi thanks to substitute Olivier Giroud's late free-kick, after an Ethan Ampadu own goal and Loic Nego's sumptuous volley had put the hosts a goal ahead.
BATE Borisov qualified alongside Chelsea after winning 3-1 at rock-bottom PAOK.
Alexandre Lacazette confirmed Arsenal's dominance of Group E with the only goal of a low-key 1-0 win over bottom side Qarabag, while second-placed Sporting Lisbon cruised past Vorskla Poltava 3-0.
Malmo are in the knockout stages after snatching a 1-0 win at Besiktas that saw the Swedes leapfrog their Turkish hosts in the extremely tight Group I.
All four teams in the group were in contention for qualification on Thursday, but Genk managed to hold on to first place after hammering Sarpsborg 4-0.
Sevilla took top spot in Group J from Krasnodar thanks to a 3-0 win, while Rennes pipped Astana to the knockout rounds with a 2-0 victory.
Bayer Leverkusen ensured first place in Group A with a 5-1 hammering of Larnaca, while Zurich drew 1-1 at Ludogorets.
Results: Group A: AEK Larnaca: 1 lt to Bayer Leverkusen: 5; Ludogorets: 1 drew with FC Zurich: 1.
Group B: Celtic: 1 lt to Salzburg: 2; RB Leipzig: 1 drew with Rosenborg: 1.
Group C: FC Copenhagen: 0 lt to Bordeaux: 1; Slavia Prague: 2 bt Zenit St Petersburg: 0.
Group D: Dinamo Zagreb: 0 drew with Anderlecht: 0; Spartak Trnava: 1 bt Fenerbahce: 0.
Group E: Arsenal: 1 bt Qarabag: 0; Sporting Lisbon: 3 bt Vorskla Poltava: 0.
Group F: Dudelange: 0 drew with Real Betis: 0; Olympiakos: 3 bt AC Milan: 1.
Group G: Villarreal: 2 bt Spartak Moscow: 0; Rapid Vienna: 1 bt Rangers: 0.
Group H: Lazio: 1 lt to Eintracht Frankfurt: 2; Marseille: 1 lt to Apollon Limassol: 3.
Group I: Genk: 4 bt Sarpsborg: 0; Besiktas: 0 lt to Malmo: 1.
Group J: Sevilla: 3 bt Krasnodar: 0; Akhisar Belediyespor: 0 drew with Standard Liege: 0.
Group K: Dynamo Kiev: 0 lt to Jablonec: 1; Rennes: 2 bt Astana: 0.
Group L: Vidi: 2 drew with Chelsea: 2; PAOK: 1 lt to BATE: 3.