Extra-time goals by Saúl Ñíguez and Koke in Tallinn ensured Atlético snatched the trophy from Real Madrid.
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Real Madrid 2-4 Atlético Madrid (aet)
(Benzema 37, Ramos 63pen; Costa 1 79, Saúl 98, Koke 104)
Real Madrid's hold on the UEFA Super Cup was ended by their neighbours, who became the first UEFA Europa League holders to win the season-opening showpiece since 2012, when they had done it themselves.
Beginning life after Zinédine Zidane and Cristiano Ronaldo, Real were hoping to make it three UEFA Super Cups in a row to add to their hat-trick of UEFA Champions League triumphs, and in doing so join Barcelona and AC Milan on five titles. But they were denied in Tallinn, Atlético becoming the only team to win on their opening three UEFA Super Cup appearances.
Their previous victories in 2010 and 2012 were the only time the UEFA Europa League winners had lifted the UEFA Super Cup since the UEFA Cup was rebranded, and Atlético were ahead inside 50 seconds as Diego Costa scored the competition's fastest-ever goal. Karim Benzema levelled in the 27th minute and just past the hour Sergio Ramos converted a penalty, only for Costa to strike again with 11 minutes left to force extra time.
Eight minutes in Saúl Ñíguez's spectacular strike gave Atlético a lead added to by Koke and in the first one-city UEFA Super Cup, they had at least some revenge for their 2014 and 2016 UEFA Champions League final defeats by their neighbours.