Zinedine Zidane's managerial record in finals remains unblemished.
The victory gives Zidane nine trophies as Real Madrid manager and maintains his perfect record in title-deciding matches with the club.
The match may never have reached that point were it not for a tactical foul from Federico Valverde in the 115th minute. The Uruguayan midfielder hacked down Alvaro Morata when the Atleti striker was clean through on goal in the waning minutes of extra time, earning a red card that arguably saved the game for his side.
"I said sorry to Alvaro," Valverde explained after the match. "It's not good to do what I did, but I was the last man."
The Super Cup featured four teams this year, as last season's La Liga and Copa del Rey winners, Barcelona and Valencia, were beaten by the two Madrid sides in the semifinals of the revamped competition.