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The Barcelona superstar picked up the ball midway inside the Brazil half and weaved past four defenders before firing a low shot into the bottom-right corner with just a minute of added time to play.
It was Messi's first ever goal against Brazil and allowed Argentina to record their first win against their old enemies since June 2005.
"It's always important to win and this victory is even more important because it's against a direct rival and it gives us confidence," said Messi.
"My goal was important because it enabled us to beat Brazil."
Messi's strike also allowed coach Sergio Batista to celebrate victory in his first game in charge since he was confirmed as the long-term successor to Diego Maradona.
|Argentina's coach Sergio Batista (L) shakes hands with Brazil's coach Mano Menezes before their teams' friendly football match at Khalifa Stadium in Doha on November 17, 2010. AFP|
For Brazil it was a first defeat in four matches for new coach Mano Menezes, who had led his country to victories in his first three games at the helm and had not previously seen his team concede a goal.
"It was a very close match but we showed inexperience in the manner in which we conceded the goal," said Menezes.
Both South American giants are rebuilding after disappointing World Cups and they will resume hostilities in La Plata, Argentina on December 19.
The Albiceleste were second-best for much of the first half, as Brazil impressed with their slick approach play, and Batista will have been delighted to secure a famous win after the 1-0 loss to Japan in their previous outing.
AC Milan forward Ronaldinho was making his first Brazil appearance since April 2009 and although he illuminated the game with some classy touches, he could not prise open the Argentine defence.
Clattering tackles were a recurring feature of the encounter and a glut of second-half substitutions seemed set to usher the game towards an anti-climactic conclusion.
A pitch invader who completed a hasty circuit of the pitch raised the crowd from their slumber with 10 minutes to play and Messi's magical intervention made sure that a forgettable encounter concluded in unforgettable fashion.
Messi's early touches had drawn roars of encouragement from the crowd, but the reigning World and European Footballer of the Year initially found his route to goal blocked by the imposing form of Benfica centre-back David Luiz.
Brazil's twinkle-toed attacking triumvirate of Robinho, Ronaldinho and 18-year-old Santos starlet Neymar quickly demonstrated their understanding and the early chances of note all fell to the five-time world champions.
Dani Alves cracked a shot against the crossbar after a one-two with Luiz, while Ronaldinho tested goalkeeper Sergio Romero with an instinctive back-heel following a corner from Neymar that was only partially cleared.
Messi grazed the left-hand post with a rasping shot shortly before half-time, but Brazil goalkeeper Victor's only prior involvement had been a double save from Gonzalo Higuain rendered irrelevant by the linesman's flag.
Napoli striker Ezequiel Lavezzi added industry and energy to the Argentine attack after replacing Higuain at the interval.
He scampered down the right flank early in the second half before teeing up club-mate Javier Pastore, but although the midfielder's strike appeared to hit Thiago Silva on the arm, the referee was unmoved.
Brazil were then aggrieved when the referee played advantage after Neymar was chopped down on the edge of the Argentina box, as Robinho had strayed into an offside position and the flag went up when the ball came to him.