Diego Costa struck in the first minute of the match before Karim Benzema restored parity in 27th minute. Sergio Ramos gave Real a 2-1 lead from the spot but Costa leveled to send the match into extra time.
Saul Niguez and Koke scored in extra time to give Diego Simeone side victory as Real conceded four goals for the first time since 2015.
Sergio Ramos and Diego Costa were back to their antagonising best in the UEFA Super Cup but it was a Saul wonder goal that made sure Atletico Madrid lifted the trophy.
The two sides will now turn their attention to Spanish La Liga which gets underway this weekend with Real playing Getafe on Sunday while Atletico will take on Valencia on Monday.
Diego Simeone has said in the past that nothing will make up for Atletico losing two Champions League finals against their bitter rivals but this was minor revenge with Real Madrid looking ragged at times, suggesting they have paid the price for not strengthening in the summer after the sale of Cristiano Ronaldo.
-Dailymail