After last week's first leg at the Calderon ended 1-1, expectations of an entertaining spectacle were high when new signing Neymar, who came off the bench to head the equaliser in Madrid, was included in the starting lineup for the first time since joining from Santos. (Agencies)
World Player of the Year Lionel Messi was also back from injury but both struggled to cope with the visitors' muscular tactics in what turned out to be a poor quality game littered with fouls including the dismissal of Atletico fullback Filipe Luis in the 81st minute.
Messi smashed a penalty against the crossbar in the 89th minute after Miranda had bundled substitute Pedro over in the area but Atletico, looking to catch Barca on the break, had the clearer chances from open play.
Arda Turan skipped into the area shortly before halftime and belted the ball toward goal but Valdes flung out an arm and diverted it to safety.
David Villa, playing against the club he left in the close season, drew another brilliant stop from his Spain team mate in the 56th minute, Valdes diving full length to tip his curling effort from just outside the box around the post.
Filipe Luis had been tangling with Brazilian compatriot Daniel Alves all night and another incident led to him being shown a straight red card before Messi saw his penalty ricochet back off the bar.
Barca's triumph was the first time any club has claimed the Super Cup without winning either leg and a first trophy for Barca's new coach Gerardo Martino, who replaced the ailing Tito Vilanova last month.
Jose Mourinho's Real Madrid beat Barca, who now have 11 Super Cups overall, to win last year's competition on away goals after the two-legged tie ended 4-4 on aggregate.
Barca won three in a row under Pep Guardiola from 2009-2011, while Atletico last won in 1985 when they beat Barca.
Played between the La Liga champions and the King's Cup winners, the Super Cup typically serves as the season opener but this time falls after two rounds of La Liga, in which both Barca and Atletico won their opening matches.
The last time the Cup winners beat the league champions was in 2007 when Sevilla overcame Real Madrid.
After last week's first leg at the Calderon ended 1-1, expectations of an entertaining spectacle were high when new signing Neymar, who came off the bench to head the equaliser in Madrid, was included in the starting lineup for the first time since joining from Santos.