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Paris -Arsene Wenger's Arsenal secured top spot in Europa League Group H on Thursday despite slumping to a 1-0 defeat at Cologne, while AC Milan reached the last 32 by thrashing Austria Vienna.
But the Gunners succumbed to a 62nd-minute penalty from Sehrou Guirassy after the French striker tumbled to ground inside the area under a challenge from Mathieu Debuchy.
Cologne, winless through 12 Bundesliga matches this season, climbed to second with one match to play, as a 0-0 draw between BATE Borisov and Red Star Belgrade in Belarus confirmed Arsenal's status as group winners.
"We've lost a game in which Cologne had one shot on goal other than the penalty," said Wenger. "We were always missing that little something to get the goal. Cologne defended with spirit and for them it's turned out to be the perfect night."
Seven-time European champions Milan wrapped up first place in Group D with a 5-1 win over Austria Vienna at the San Siro.
Christoph Monschein put the visitors ahead in Italy, but Vincenzo Montella's team roared back with Andre Silva and Patrick Cutrone both netting twice along with a goal from Ricardo Rodriguez.
Atalanta sealed their spot in the knockout phase as Bryan Cristante and Andreas Cornelius notched two goals apiece to thump a listless Everton 5-1 at Goodison Park.
Robin Gosens added another with a terrific dipping volley, with Sandro Ramirez scoring his first Everton goal as the Toffees crashed to a fourth defeat in five group outings.
"There was nothing riding on the game, but it's our pride. It's not nice to lose games. It's very disappointing and upsetting," Everton captain Wayne Rooney told BT Sport.
Nabil Fekir notched his 13th goal of the season for Lyon in a 4-0 rout of Cypriots Apollon Limassol as the French side joined Atalanta in advancing from Group E.
Mario Balotelli scored twice as Nice moved into the last 32 following a 3-1 victory over Zulte Waregem of Belgium, with Lazio dropping their first points in Group K after a 1-1 draw at home to Vitesse Arnhem.
Marseille snatched a 93rd-minute equaliser courtesy of an own goal from Wilfried Moke in a 1-1 draw at Konyaspor to stay ahead of their Turkish opponents in the race for second behind Salzburg, 3-0 winners over Vitoria Guimaraes, in Group I.
"Miracles don't happen by chance," said Marseille coach Rudi Garcia, whose side saw Jordan Amavi dismissed 10 minutes from time.
"Like in the last match, the team believed in itself until the end despite being a man down."
Villarreal progressed to the knockout stages as Democratic Republic of Congo striker Cedric Bakambu netted a brace to seal a 3-2 victory over Astana in Kazakhstan.
Surprise Swedish side Ostersund - coached by Englishman Graham Potter - extended their run in Europe into the New Year with a 2-0 home win over Ukrainians Zorya Luhansk.
Veteran Spain striker Aritz Aduriz scored two penalties in Athletic Bilbao's 3-2 win over Hertha Berlin to leave the Basque club with their fate in their own hands heading into the final round of fixtures.
Europa League results on Thursday:
Group A
Astana (KAZ) 2 (Kabananga 22, Twumasi 88) Villarreal (ESP) 3 (Raba 40, Bakambu 65, 83)
Maccabi Tel Aviv (ISR) 0 Slavia Prague (CZE) 2 (Husbauer 45+1, 54)
Group B
Partizan Belgrade (SRB) 2 (Tawamba 12, Ozegovic 53) Young Boys (SUI) 1 (Ngamaleu 25)
Skenderbeu (ALB) 3 (Lilaj 18, James 52, Sowe 58) Dynamo Kiev (UKR) 2 (Tsygankov 16, Rusyn 90)
Group C
Braga (POR) 3 (Marcelinho 1, Fransergio 82, 90+3) Hoffenheim (GER) 1 (Uth 74)
Ludogorets (BUL) 1 (Marcelinho 65) Istanbul Basaksehir (TUR) 2 (Visca 20, Frei 27)
Group D
AC Milan (ITA) 5 (Rodriguez 27, Silva 36, 70, Cutrone 42, 90+3) Austria Vienna (AUT) 1 (Monschein 21)
AEK Athens (GRE) 2 (Gorgon 8, 26) Rijeka (CRO) 2 (Araujo 45+2, Christodoulopoulos 55)
Group E
Everton (ENG) 1 (Ramirez 71) Atalanta (ITA) 5 (Cristante 12, 64, Gosens 87, Cornelius 88, 90+4)
Lyon (FRA) 4 (Diakhaby 29, Fekir 32, Diaz 66, Maolida 90) Apollon Limassol (CYP) 0
Group F
Sheriff Tiraspol (MDA) 1 (Jairo 11) Zlin (CZE) 0
Lokomotiv Moscow (RUS) 2 (Farfan 17, 51) FC Copenhagen (DEN) 1 (Verbic 31)
Group G
Lugano (SUI) 1 (Carlinhos 50) Hapoel Beer Sheva (ISR) 0
Viktoria Plzen (CZE) 2 (Petrzela 49, Kopic 76) FCSB (ROU) 0
Group H
BATE (BLR) 0 Red Star Belgrade (SRB) 0
Cologne (GER) 1 (Guirassy 62-pen) Arsenal (ENG) 0
Group I
Konyaspor (TUR) 1 (Skubic 82-pen) Marseille (FRA) 1 (Moke 90+3-og)
Salzburg (AUT) 3 (Dabbur 26, Ulmer 45+1, Hwang 67) Vitoria Guimaraes (POR) 0
Group J
Athletic Bilbao (ESP) 3 (Aduriz 35-pen, 66-pen, Williams 82) Hertha Berlin (GER) 2 (Leckie 26, Selke 36)
Ostersund (SWE) 2 (Grechyshkin 40-og, Ghoddos 77) Zorya Luhansk (UKR) 0
Group K
Lazio (ITA) 1 (Alberto 42) Vitesse Arnhem (NED) 1 (Linssen 13)
Nice (FRA) 3 (Balotelli 5-pen, 31, Tameze 86) Zulte Waragem (BEL) 1 (Hamalainen 80)
Group L
Rosenborg (NOR) 0 Real Sociedad (ESP) 1 (Oyarzabal 90)
Zenit St Petersburg (RUS) 2 (Poloz 16, Rigoni 43) Vardar (MKD) 1 (Blazevski 90+3)
