Federico Valverde was shown a straight red card in the second half of extra time when he cynically brought down Alvaro Morata after the Atletico man had raced in behind the Real back line.
Atleti did nothing with the free kick from just outside the box and ultimately couldn’t make their advantage count before the match headed to penalties.
In the shootout, Saul and Thomas each failed to convert their chances and Real went perfect from the spot to secure the victory.
It was the first year that the competition was expanded to include four teams and was moved to a neutral site.
Real Madrid had most recently won the title in 2017, when they beat Barcelona 5-1 over two legs.