Gareth Bale delivered a cross from the right and Benzema headed past Jan Oblak at the far post.
The winger has registered six assists against Atletico down the years, including one in the 2015-16 Champions League final and one in the most recent meeting between the two sides, but he has generally found things more hard against La Rojiblancos.
With the scores 2-2 after 90 minutes the game went to extra time, and it took two beautifully crafted goals to give Diego Simeone's men the win over their crosstown rivals. Real Madrid welcome Getafe on Sunday evening.
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The game will be played at the Lillekula Stadium in Tallinn, Estonia. In the United States and Canada Eastern Time Zone that start time will be 3 p.m., noon in the Pacific time zone.
Wednesday night's thriller at Tallinn's A. Le Coq Arena swung back and forth and into extra time, with Diego Costa netting twice for Atletico, before Europa League holders Atletico finally got on top of triple-Champions League winners Madrid to take an extra sweet victory given all the history and local rivalry involved.
Defender Ramos, the scourge of Atletico Madrid in recent years, stepped up and sent Oblak the wrong way.
Pogba tight-lipped over United situation for fear of being fined
When asked after the game whether he was happy at the club, Pogba said, in remarks published on Sunday, that "There are things I can not say, otherwise I will get fined".
"We are at a time when new players arrive to improve the team".
Luka Modric's agent has opened the door to a potential move to Inter, insisting the Real Madrid midfielder is enthused by the idea of playing for the Serie A side.
It is the seventh UEFA Super Cup match between two clubs from same country, and the fifth all-Spanish affair.
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