Atletico qualified in second spot in the group with seven points, ahead of FC Porto on five, while Milan finished last on four points after going down 2-1 at home to Liverpool in the UEFA Champions League.
Atleti’s triumph came amid high tensions in the second half in Oporto, with Atletico’s Yannick Carrasco sent off in the 67th minute for an off-the-ball incident, before Wendell also saw red for Porto for a raised elbow three minutes later.
The Spanish champions were leading 1-0 at the time from Antoine Griezmann’s 56th-minute goal, but added two more late goals from Angel Correa and Rodrigo de Paul to seal their progress. Sergio Oliveira netted a late consolation from the spot for Porto.
Atletico boss Diego Simeone said: “The game had everything sendings off, chances. Football, how beautiful.
He added: “Ive been at this club for ten years and the team always ends up exciting me in new ways.”
Milan needed to beat the Reds and hope that the Porto-Atletico game finished as a draw, but couldn’t hold up their end of the bargain.
Fikayo Tomori had put the Rossoneri ahead in the 28th minute but Mohamed Salah levelled eight minutes later with a cool finish from a rebound. Divock Origi netted a 55th minute winner with a header from a similar rebound.
In Group A, Manchester City were beaten 2-1 by RB Leipzig but had already finished top, with Paris Saint-Germain getting past Club Brugge 4-1 with doubles from Kylian Mbappe and Lionel Messi.
In Group C, Sporting Lisbon got through despite a 4-2 loss to Ajax Amsterdam, with Borussia Dortmund finishing third with a 5-0 rout of Besiktas.
In Group D, Real Madrid secured top spot with a 2-0 home victory over Inter Milan with goals from Toni Kroos and Marcos Asensio, while Sheriff Tiraspol finished third with a 1-1 draw at Shakhtar Donetsk.