The capital outfit should have been home and dry after a dominant first half against the 10-man visitors, but Messi's free kick saw Madrid forced to grind out a tense result.
Los Blancos triumphed on away goals after the tie finished 4-4 on aggregate, but it should have been a much wider margin after a shambolic defensive start from Tito Vilanova's men.
A missed clearance from Javier Mascherano saw Gonzalo Higuain gifted the opener, and an outrageous move from Cristiano Ronaldo on Gerard Pique put him in position to make it 2-0 after 19 minutes.
Adriano's red card just before half an hour seemed to signal the the end of Barca's hopes, but Lionel Messi dragged the club back to its feet with a fantastic free kick on the stroke of halftime.
The second half was far more tense as a much-improved Barca had chances to score again, but there was no way back for the visitors as Madrid hung on to claim the first trophy in Spain this season.
Pepe returned from a concussion to start alongside Sergio Ramos in defense, but there was no place for new signing Luka Modric, who began the game on the bench.
An injury to Dani Alves during the warmup forced Tito Vilanova to draft Jordi Alba in at left back, with Adriano shifting to the opposite flank. Carles Puyol was another notable absentee after fracturing a cheekbone in the 2-1 win over Osasuna on the weekend.
The Barcelona captain may have well had a thing or two to say after a dreadful defensive opening that saw Madrid storm into a two goal lead after 20 minutes.
Mascherano had already allowed Higuain to slip past him for an early one-on-one that was saved by Victor Valdes, and the Argentine gifted his compatriot an even greater chance in the 11th minute, when his missed attempt at a clearance allowed the striker to steal in and slot home the opener.
It went from bad to worse for Barca eight minutes later, as Madrid struck again after pouncing on another lapse at the back. Pique was left bamboozled by a heel flick from Ronaldo, who advanced on goal and had time to steady himself before blasting in via the leg of Valdes.
Valdes was called into action once more to deny Higuain, who was again able to get behind the defense, while Madrid saw a third goal questionably disallowed for an infraction after Pepe nodded in a free kick.
The visiting side was all at sea, and the chances seemed to be virtually extinguished just before the half hour mark when Adriano was shown a straight red card for pulling down Ronaldo on a clear break towards goal for the Portuguese.
Vilanova was forced to throw on Martin Montoya for Sanchez in a bid to shore up his defense as Madrid continued to dominate. Sami Khedira’s volley was thwarted from point blank range by Valdes, before a last ditch challenge from Mascherano halted Higuain as he bore down on goal.
However, there were a few signs of life from Barca as the first half drew to a close. Montaya came within inches of connecting with Andres Iniesta’s low cross, and then, in stoppage time, a moment of magic from Messi gave the visitors a fighting chance.
The Argentine took charge of a free kick after Xavi was felled 30 yards from goal, and bent a breathtaking effort around the wall, past the outstretched arm of Iker Casillas and into the back of the net.
Still, Madrid nearly responded in the dying embers of the first half. Ronaldo’s 35-yard drive bounced inches wide, and Higuain also narrowly missed, after cutting onto his left foot deep inside the area.
Barca headed into the break knowing that it still had a lot of work to do, and looked to wrest control from the home side as the second half unfolded.
Madrid seemed content to sit back and protect the advantage, which allowed the Blaugrana the chance to dictate proceedings with their famed tiki-taka football.
Their improved endeavor was almost rewarded on the hour mark, after a searching ball from the back by Mascherano was taken in stride brilliantly by Pedro, who saw his shot met by an equally fantastic save from Casillas.
The Spanish forward had another opening moments later after sneaking in on the right, but Casillas was again alert to stop him from poking home at the near post.
Madrid was far from ruthless, but still harbored a significant threat on the break. Khedira nearly scored a third after beating multiple defenders en-route to goal, but Valdes was able to block strongly.
Alba was thwarted at the last by a great challenge from Ramos, before Higuain was allowed through on goal for the umpteenth time, but could not finish the chance as his effort bounced off the base of the post.
Late openings appeared for both sides, but no more goals were forthcoming as Madrid held on to claim the Supercopa, and set the pace for what is sure to be a enthralling season in Spain.
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