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Three-time Champions League winner United needed to beat Bayern Munich at home and hope for a favorable result in the other Group A game but lost 1-0 to the six-time winner.
Sevilla, the undisputed kings of the Europa League, have now won all seven of the finals they have played in the competition, and are well-versed in the drama of the occasion, having seen their opponents score first in the last four finals
Goalkeeper Yassine Bounou played in Kochi in a pre-season friendly for Girona FC in 2018.
Danish forward Martin Braithwaite grabbed the decisive goal with a scrappy diving header early in the extra period.
The victory took Atletico on to 41 points after 16 games, four clear of second-placed Real Madrid who have played 18.
Meanwhile, Valencia are still without a win this season after being held to a 2-2 draw at neighbours Levante.
With this win, Lionel Messi overtook Andres Iniesta as Barca's most decorated player with 33 trophies to his name.
Philippe Coutinho scored his first league goal since returning to Barcelona to help his side draw 1-1 at home to an excellent Sevilla side in La Liga on Sunday.
The Catalans are top of the standings on 65 points from 30 games but second-placed Real Madrid, with 62, can go above their rivals if they beat Real Sociedad away on Sunday due to their superior head-to-head record.
Sevilla beat city rivals Real Betis 2-0 on Thursday with the help of a controversial penalty and a touch of class from Argentine winger Lucas Ocampos.
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