José Mourinho's side ruthlessly dispatched Zorya Luhansk to go through, but Tottenham suffered a significant defeat.
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AZ Alkmaar, Copenhagen, Gent, Feyenoord, LASK and Rennes all booked places in the last 16 as group winners while Roma assured themselves of a top-two finish – but the outlook is less clear-cut for Tottenham after their shock reverse away to Mura.
UEFA.com rounds up the Thursday night action.Play Europa Conference League Predictor
How qualifying for the knockouts works
The eight group winners automatically go through to the last 16. Additional knockout round play-offs will then be played before the round of 16 between the eight group runners-up and the third-ranked teams from the UEFA Europa League groups.
Tammy Abraham's outrageous overhead kick topped off a superb night for Roma, who secured progression from Group C. The hosts' ruthless mood was evident from the start as Carles Pérez tapped in Stephan El Shaarawy's beautiful cross on 15 minutes. Nicolò Zaniolo was positive all night and drilled in the second before Dmytro Matsapura saved Jordan Veretout's spot kick. Zaniolo's driving influence set up Abraham for the third and the chances kept flowing until the striker's bicycle-kick brilliance.
Key stat: Roma are now unbeaten in 16 matches at the Stadio Olimpico in European competition.
Spurs' qualification hopes hang in the balance after they were beaten by the last kick of the game in Slovenia. Tomi Horvat fired a superb opener for the home side, who were seeking their first points in the section, and Ryan Sessegnon's first-half red card increased the chances of an upset. Harry Kane looked to have saved the visitors only for Amadej Maroša to break away and fire a dramatic winner with the aid of a deflection.
Key stat: Mura had lost their last six European matches and never taken a point in the group stage of a UEFA club competition before this game.
Confirmed group winners
AZ Alkmaar (NED)
Best of the rest
- Cyriel Dessers struck has second goal deep into added time to earn Feyenoord the draw they needed at Slavia Praha to win Group E.
- Gent secured top spot in Group B before their match at Anorthosis had kicked off after Partizan were beaten 1-0 at Flora.
- Copenhagen were another side to progress as group winners thanks to a 4-0 victory at Lincoln Red Imps and a goalless draw between nearest challengers Slovan Bratislava and PAOK.
- Tottenham's defeat meant a point at home to Vitesse was enough for Rennes to wrap up Group G, and they earned it courtesy of Gaëtan Laborde's hat-trick in a 3-3 draw.
- A draw was also the tonic for AZ Alkmaar, with their 1-1 result away to Jablonec clinching first place in Group D.
- LASK were the last of the six to rubber-stamp their position at the summit, Sascha Horvath scoring their 89th-minute winner to sink second-placed Maccabi Tel-Aviv.
- A win for Basel and draw for Qarabağ means the already-qualified pair head into their Matchday 6 meeting in Switzerland level on points in Group H.
Assured of a top-two finish
Maccabi Tel-Aviv (ISR)
All Matchday 5 results
Group A: HJK Helsinki 1-0 Alashkert, Maccabi Tel-Aviv 0-1 LASK
Group B: Anorthosis Famagusta 1-0 Gent, Flora Tallinn 1-0 Partizan
Group C: Roma 4-0 Zorya Luhansk, Bodø/Glimt 2-0 CSKA-Sofia
Group D: Jablonec 1-1 AZ Alkmaar, Randers 2-1 CFR Cluj
Group E: Slavia Praha 2-2 Feyenoord, Maccabi Haifa 0-1 Union Berlin
Group F: Slovan Bratislava 0-0 PAOK, Lincoln Red Imps 0-4 Copenhagen
Group G: Mura 2-1 Tottenham, Rennes 3-3 Vitesse
Group H: Kairat Almaty 2-3 Basel, Qarabağ 2-2 Omonoia