Champions League: Atletico Seal Qualification, Bayern Beat Tottenham
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Kieran Trippier had a second-minute penalty brilliantly saved by Lokomotiv goalkeeper Anton Kochenkov at the Wanda Metropolitano, but Joao Felix made no mistake from the spot a quarter of an hour later.
Atletico wasted a string of chances and Alvaro Morata had a goal ruled out by VAR for offside.
But their place in the knockout rounds was secured when centre-back Felipe volleyed home Koke's cross after a short corner routine.
Cristiano Ronaldo scored his second Champions League goal of the season as Juve, who were already sure of top spot, saw off Leverkusen 2-0 in Germany in the other Group D game.