Following the 1-1 draw in the first-leg, the Catalans were left to thank goalkeeper Victor Valdes for preserving their advantage as he pulled off incredible saves from Arda Turan and David Villa either side of half-time.
Barca should have then sealed victory on the night themselves as after Filipe Luis was sent off for Atleti, Lionel Messi fired a late penalty off the bar.
"Victor has always had this characteristic which makes a goalkeeper for a big team," Barca boss Gerardo Martino told a press conference afterwards.
"They had two shots on goal and he made the saves."
Martino had handed a first start to Neymar as the Brazilian and Lionel Messi lined up for the first time in a competitive match since the former's switch from Santos.
And he admitted that the South American duo have plenty to work on as a partnership.
"Separately they have played quite well. It is true that they didn't combine a lot and they didn't find each other.
"Neymar was a bit closed off on the wing and when Leo came deep he drifted to the other side. Sometimes they were too far apart to combine but they will manage to do so with time."
Having weathered an early Barca early storm though, Atleti started to gain a foothold and had the two best openings of the opening period.
Firstly Koke failed to connect properly when he was teed up at the edge of the box allowing Valdes to save easily before the Barca keeper made a stunning save to turn behind Arda's sweetly struck volley.
Valdes was called upon again after the break as he parried Villa's curling effort from the edge of the area as Atleti went in search of the away goal they needed to stay alive in the tie.
And Atleti boss Diego Simeone was left to rue his side's wasted opportunities.
"The match was how I imagined it on both sides," he said.
"They played as they have for many years and we continue to grow, with pride and knowing we can play.
"We had more chances but we couldn't take them."
The more the visitors pushed forward though, the more they were susceptible to the Barca counter-attack and the Catalans passed up a host of opportunities to put the tie to bed.
Neymar was the biggest culprit as he squared when he ought to have gone for goal himself at the back post from Dani Alves' cross midway through the second-half.
Atleti were then reduced to 10 men when Luis saw a straight red card after he clashed with Alves off the ball on 80 minutes.
And Simeone's men were further infuriated by referee David Fernandez Borbalan when he adjudged that Pedro had been felled by a combination of Juanfran and Miranda two minutes from time.
Messi smashed the resultant spot-kick off the bar to ensure the game finished goalless.
However, it mattered little as the hosts comfortably saw out the final few minutes to claim their fourth Super Cup in the past five years.