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 line-up for the first time since joining from Santos.
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 81st-minute dismissal of Atletico full-back Filipe Luis.
Messi smashed a penalty against the crossbar in the 89th minute after Miranda had bundled substitute Pedro over in the area but Atletico, constantly 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.
"This Atletico team is a team of winners, who fight and battle and are a very tough opponent," Barca centre back Javier Mascherano told Spanish television broadcaster TVE.
"It was a very close match," added the Argentine. "Atleti make things very difficult for you and we have to congratulate them. They compete very well."
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.
Martino got the better of his Atletico counterpart and Argentine compatriot Diego Simeone but Barca's inability to create scoring opportunities will be of some concern as they bid for a fifth La Liga crown in six years.
They will find out their opponents in the Champions League group stage in Thursday's draw before bidding for a fifth success in Europe's elite club competition.
Atletico's ability to nullify Messi and snuff out any attacking threat from elsewhere was worryingly reminiscent of last season's semi-final against Bayern Munich, which Barca lost 7-0 on aggregate.
"When there is a title up for grabs the important thing is to win it," Martino said.
"We need more pace, more precision and we need to attack the space so that we avoid running into the opposition defence.
"But considering the season has only just begun I don't think it's too bad. Sometimes a team needs results like this to find its form."
Simeone was proud of his players but lamented their inability to take their chances.
"We had two clear opportunities and in these matches you have to put them away," the former Argentina and Atletico player said. "Valdes was very good."
Barca now have 11 Super Cups, winning four of the last five.
Jose Mourinho's Real Madrid defeated them last year to break their run of three trophies under Pep Guardiola from 2009-2011.
Played between the La Liga champions and the Copa del Rey winners, the Super Cup typically serves as the season opener but this time came after two rounds of La Liga.