The home side dominated the possession in the first period, but it was Atletico that passed up a couple of golden chances to open the scoring.
Neither side could find the back of the net in the second period as Barcelona claimed the trophy on away goals.
Here, Sports Mole dissects the 90 minutes of action between the two La Liga rivals.
On target: 1
On target: 3
Was the result fair?
On the balance of play, Atletico will feel that they deserved something more from the match this evening. Barcelona, as expected, dominated the possession, but they did not really threaten the away side's goal. Atletico passed up two golden opportunities to score the decisive goal in the first period, but ultimately Victor Valdes denied them the chance to claim the first trophy of the season.
Gone are the days that Barcelona just have to turn up to beat Atletico. If they were up against any other Spanish side this evening, Real Madrid aside, they would probably have won comfortably. However, their lack of a Plan B became evident in the second period when they could not find a way through the Atletico defence. They have won the trophy, but there is much to ponder for the league champions in the new campaign.
There is no question that Atletico are getting closer to Barcelona. In both legs of the Super Cup, there was simply nothing to choose between the two teams. Atletico were forced to concede possession for long spells, but they were able to nullify the threat from the Catalan outfit. Even though they were defeated on away goals, the capital outfit will take plenty from the match this evening.
Sports Mole's man of the match
Victor Valdes: The fact that the Barcelona goalkeeper has been handed this accolade tells you everything that you need to know. He made two notable saves during the 90 minutes - one was outstanding, the other was world-class as he somehow managed to tip a Turan effort over the crossbar from close range in the first period. Could he be in contention to replace Iker Casillas as Spain's goalkeeper at next summer's World Cup?
Biggest gaffe of the match
Koke might have been one of Atletico's best players last season and indeed in the early stages of the new campaign, but he passed up a glorious chance to send them into the lead in the first period. When presented with the ball just inside the box, he stroked a tame effort into the arms of Valdes, much to the frustration of his teammates.
I would not think that Fernandez Borbalan has ever officiated such a difficult match. The Spaniard did well to keep a lid on proceedings in the first period, but was forced to issue a number of bookings in the second half. He was forced to rely on his assistant when dismissing Luis, but on first glance, it did appear to be the correct decision. The penalty award was slightly harsh, but justice was done when Messi hit the crossbar. In terms of the dismissal of Turan, who had been substituted, Borbalan again relied on his colleagues.
Barcelona: The league champions resume domestic duties this weekend with a trip to Valencia on Sunday.
Atletico: Atletico also return to league action on Sunday when the capital outfit travel to Real Sociedad, who secured their spot in the Champions League group stages this evening.