Lyon routed Apollon 4-0 and Atalanta hammered Everton 5-1 in Goodison Park, leaving the Premier League side winless, to confirm their dominance in Group E. Both winners have secured a spot in the knockout stage. Atalanta hosts Lyon in their final group stage encounter on Dec 7 to decide which team finishes top.
Elsewhere, Villarreal advanced from Group A with a 3-2 at Astana, Sweden's Ostersund beat Zorya Luhansk 1-0 in a match between the pacesetters in Group J to qualify, while Salzburg made the next stage from Group I with a 3-0 victory over Portugal's Vitoria Guimaraes.
Mario Balotelli's two strikes help Nice to qualify from Group K and Real Sociedad became the second team from Group L after Russia's Zenit to get through after a 1-0 win at Rosenborg. In Group C, Braga is through to the next stage after a 3-1 win over Hoffenheim, and Partizan Belgrade qualified with a 2-1 win over Young Boys, the second team from Group B to make it after Dynamo Kiev.
Here's a look at Thursday's action:
BACK TO WINNING
Coming off two goalless draws in Europe's second tier competition, and a Serie A loss to Napoli on Saturday, Milan's start to the game against Austria Vienna looked like another dismal night for Italy's biggest spender in the offseason.
Vienna forward Christoph Monschein beat the offside trap in the 21st minute to shock the hosts with the opening goal of the game at San Siro.
But Milan proved its class time this time, and was quick to turn things around.
Ricardo Rodriguez equalized with a low shot just six minutes later, Silva got his first nine minutes after that and Patrick Cutrone completed Milan's rally three minutes before the break. With his second in the 70th, Silva made it six goals in five Europa League games. Cutrone finished the visitors off with his second goal in stoppage time.
The victory secured top spot in Group D for Milan.
FIRST LOSS FOR ARSENAL
Arsenal gave another dominant display in the Europa League despite manager Arsene Wenger resting the entire starting 11 that beat Tottenham 2-0 in the Premier League on Saturday.
Sehrou Guirassy scored a penalty in the 63rd minute in Cologne, against the run of play.
With recalled Danny Welbeck and Olivier Giroud up front, Arsenal held the upper hand but failed to turn their possession into victory.
Francis Coquelin hit the post in the first half in Arsenal's best chance.
Before the game, players and fans observed a minute silence that later turned into a standing ovation for the late Hans Schaefer, a former Cologne winger who won 1954 World Cup with West Germany. Schaefer died at age 90 earlier in November.
After BATE Borisov played to a 0-0 draw against Red Star Belgrade, Arsenal tops Group H with 10 points. Red Star and Cologne trail by four points, Borisov is another point behind.
VILLARREAL HAUNTS ASTANA
Substitute forward Cedric Bakambu struck twice against a Kazakh side that had been undefeated at home in its previous 17 matches in European competitions. The last team to win there was none other than Villarrealm in the 2014-15 Europa League playoffs.
A constant threat, Bakambu netted his first goal in the 65th minute after a fast counter-attack and added his second from the edge of the area in the 83rd.
Junior Kabananga put the hosts ahead in the 22nd before Daniel Raba started Villareal's revival with a 39th minute equalizer.
Patrick Twumasi scored the second for Astana two minutes from time.
Villareal tops Group A on 11 points, with Astana four points behind.
BALOTELLI ON FIRE
Balotelli scored twice in the first half to secure a knockout spot for Nice. In a perfect start, Balotelli converted from the penalty spot, sending goalkeeper Louis Bostyn the wrong way. The striker made it 2-0 from close range in the 31st to put the hosts in control with his fourth goal in five Europa League games this season.
Adrien Tameze added a late goal for Nice, while Brian Hamalainen scored the consolation goal for Waregem.
Nice joins Group K winner Lazio in the next round, after the Italian club was held to a 1-1 draw at home by Vitesse.