A stoppage-time goal from Joao Mario completed a 6-1 win for the Portuguese side at Maccabi Haifa and edged them above PSG in Group H, despite the French side winning 2-1 at Juventus courtesy of goals from Kylian Mbappe and Nuno Mendes.
Benfica and PSG ended the group stage with the same number of points, goals scored and goal difference, with both games between the sides finishing in 1-1 draws.
Juventus dropped into the Europa League play-offs, with Maccabi eliminated.
Rico Lewis became the youngest player to score on their first start in the competition as Manchester City came from behind to beat Sevilla 3-1 in their final group game.
The right-back, aged 17 years and 346 days, smashed home the equaliser following Rafa Mir’s opener to break the record held by Karim Benzema, who was 17 years and 352 days old when he scored for Lyon against Rosenborg in 2005.
Goals from Julian Alvarez and Riyad Mahrez completed the win in Group G, although all four positions had already been decided.
Denis Zakaria scored the winner on his Chelsea debut as Graham Potter’s side finished top of Group E with a 2-1 victory over Dinamo Zagreb at Stamford Bridge.
Bruno Petkovic gave the visitors an early lead, but Raheem Sterling equalised before on-loan Juventus midfielder Zakaria struck the winner.
In the evening’s early games, Real Madrid clinched top spot in Group F with a 5-1 thrashing of Celtic.
Luka Modric and Rodrygo both scored first-half penalties before Celtic’s Josip Juranovic saw his own spot-kick saved, with Marco Asensio, Vinicius Junior and Federico Valverde also on target at the Bernabeu.
Substitute Jota scored a superb late free-kick for the outclassed visitors.
RB Leipzig also advanced to the knockout stage with a 4-0 win at Shakhtar Donetsk.