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Bayern dominated the tie, progressing with a 10–2 aggregate win following their 6–1 first-leg triumph in Bergamo.
England striker Harry Kane scored twice, including a penalty, while Lennart Karl and Luis Díaz added further goals. Lazar Samardžić netted a late consolation for Atalanta.
Atlético Madrid also advanced to the quarter-finals despite a 3–2 defeat away to Tottenham Hotspur, setting up a meeting with FC Barcelona.
Goals for Tottenham came from Randal Kolo Muani and Xavi Simons, who scored twice. Atletico’s goals were netted by Julián Álvarez and Dávid Hancko. a goal by Ademola Lookman was disallowed after a var review for offside.