Gonzalo Higuain and Cristiano Ronaldo put Madrid in control with goals inside 23 minutes at the Santiago Bernabeu to take advantage of Barcelona's poor start.
Adriano was red-carded for tripping Ronaldo as he was set to race clear on goalkeeper Victor Valdes in the 28th to further thwart the visitors' hopes.
But Lionel Messi curled home an exquisite free kick before halftime of another thrilling match between the Spanish giants with the league champions hanging on to beat the cup holders for the title.
Alex Song and Luka Modric both made their debuts for their clubs, with Madrid's first victory of the season in all competitions helping it recover from its worst start for nearly 40 years and edging it ahead of Barcelona 88-87 in wins between the ''clasico'' rivals.
It also provided coach Jose Mourinho with the last piece of silverware missing from his Spanish trophy cabinet. The Portuguese coach's 20th title means he has won every trophy available in the four leagues where he's coached - Spain, England, Italy and Portugal.
Barcelona hadn't won a trophy against Madrid at the Bernabeu since 1968 and its flat start certainly made victory look unlikely.
Madrid took advantage of its rival's worst spell of football since perhaps before Pep Guardiola took charge in 2008 early on as Higuain forced Valdes into a clutch save in the 7th before burying his next chance.
Barcelona defender Javier Mascherano missed Pepe's long ball as it fell to Higuain inside the Barcelona area for the Argentina striker to half-volley between Valdes' legs.
Mascherano's struggles continued with a booking, and Valdes was incensed with his defense in the 22nd as Higuain burst clear inside the area again to force another goal-saving stop.
A short time later, Gerard Pique failed to disrupt a long ball to Ronaldo who, while on the run, flicked it high to himself. The Portugal forward gathered his poor touch before blasting a low shot past Valdes from just inside the area to score for the fifth straight game against Barcelona.
Barcelona, which was without injured defenders Dani Alves and Carles Puyol, looked dazed and confused as Higuain nearly scored again before Barcelona finally gained some momentum when Miguel Montoya replaced Alexis Sanchez after Adriano was red carded.
Barcelona regained its composure despite being a man down before Messi curled around the outside of the defensive wall past the outstretched Iker Casillas for his 15th goal against Madrid, a club record.
Casillas made big stops on Pedro Rodriguez in the second half while Valdes stopped Sami Khedira before Song replaced Sergio Busquets in the 75th for his Barcelona debut.
Still, Madrid had chances to put the game away as Higuain hit the post in the 80th before Modric came on two days after joining from Tottenham in a transfer worth a reported $42 million.
Messi's final attempt in injury time flew wide as Madrid hung on to win its ninth Super Cup.