Lyon held off a late Athletic Bilbao comeback to earn a thrilling 3-2 victory in the pick of Thursday's late Europa League matches.
Bafetimbi Gomis, Yoann Gourcuff and Alexandre Lacazette all found the net at the San Mames to severely damage the Spaniards' chances of reaching the next round.
Group I's other game saw Hapoel Kiryat Shmona draw 1-1 at home to Sparta Prague.
Basel boosted their hopes of progressing in the competition with a 1-0 win over Videoton, while Group F leaders Genk were held to a 1-1 draw at Sporting Lisbon.
Bayer Leverkusen are into the knockout stages thanks to a comfortable 3-0 triumph against Rapid Vienna and they will be joined by Metalist Kharkiv after the Ukrainians saw off Rosenborg 3-1.
Inter Milan are also through to the next round courtesy of their 3-1 win at Partizan Belgrade.
Hannover have secured their passage out of Group L with a 3-2 victory over Helsingborg, while Levante were unable to get the win that they needed to qualify as they were held to a goalless draw at FC Twente.
Tottenham Hotspur picked up their first win of this year's tournament as a Jermain Defoe hat-trick saw them defeat Maribor 3-2 and there was also a victory for Group J leaders Lazio who beat Panathinaikos 3-0.
Thursday's Europa League results in full:
Group A: Anzhi Makhachkala 1-0 Liverpool Udinese 2-3 Young Boys
Group B: Academica 2-0 Atletico Madrid Viktoria Plzen 4-0 Hapoel Tel Aviv
Group C: Marseille 2-2 Borussia Monchengladbach Fenerbahce 2-0 AEL
Group D: Club Brugge 2-2 Newcastle United Bordeaux 1-0 Maritimo
Group E: Molde 1-2 Steau Bucharest Copenhagen 0-2 Stuttgart
Group F: AIK 1-0 PSV Eindhoven Napoli 4-2 Dnipro
Group G: Basel 1-0 Videoton Sporting 1-1 Genk
Group H: Partizan Belgrade 1-2 Inter Milan Neftchi Baku 0-1 Rubin Kazan
Group I: Hapoel Kiryat Shmona 1-1 Sparta Prague Athletic Bilbao 2-3 Lyon
Group J: Lazio 3-0 Panathinaikos Spurs 3-1 Maribor
Group K: Metalist Kharkiv 3-1 Rosenborg Bayer Leverkusen 3-0 Rapid Vienna
Group L: Hannover 3-2 Helsingborg FC Twente 0-0 Levante