Messi had a chance to put the result beyond doubt in 89th but fired his penalty kick off the crossbar to finish a forgettable night for the Argentina star yesterday.
Barcelona eventually claimed the trophy on away goals following the 1-1 draw in the opening leg last week.
Atletico's disciplined defense stifled a Barcelona's attack featuring Neymar making his first starting appearance for his new club.
And the visitors enjoyed the best scoring opportunities other than Messi's penalty attempt but weren't able to get the critical goal, mainly because of Barcelona goalkeeper Victor Valdes. Atletico's chances were hurt in the 81st when Filipe Luis was given a red card for apparently hitting Dani Alves. The scoreless draw meant Neymar's first-leg goal was the difference.
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Messi was back for Barcelona after missing one game due to a left thigh injury sustained in the opening Super Cup match last week.
But the four-time world player of the year was not his usual dynamic self, lacking his spark and finishing touch. He uncharacteristically scuffed a close-range shot off a pass from Sergio Busquets to start his off night.
Messi and Neymar had only previously been on the pitch together for seven minutes because Martino said he wanted to ease the 21-year-old Brazil striker into his new team. But those eager to see the two together were disappointed. While Messi was below par, Neymar wasn't able to exploit his speed and dribbling against Atletico's physical defense.