Barcelona wins Spanish Super Cup
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. 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. 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.
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 precision. He uncharacteristically scuffed a close-range shot off a pass from Sergio Busquets to start his off night.
Barcelona coach Gerard Martino gave Neymar his first start in his fourth official game for Barcelona since his (euro) 57-million move from Santos in June.
Messi and Neymar had only previously been on the pitch together for seven minutes, during a Barcelona's league opener, 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.
Atletico's plan to relinquish the ball and look to hit on the break worked in the first half.
Diego Costa produced Atletico's first chance on goal in the 35th when he passed for David Villa to set up Jorge ''Koke'' Resurreccion, only for the young midfielder to weakly shoot into the arms of goalkeeper Victor Valdes.
Atletico missed another chance to go ahead in the 42nd when Arda Turan drew an excellent save from Valdes.
Needing to score to offset Barcelona's away-goal advantage, Atletico dictated the pace early in the second half and shifted the action to Barcelona's area. Valdes was called upon to make another one-armed save to keep out Villa's curling effort in the 56th.
Martino sent Pedro Rodriguez on in the 65th to lift his team, and even though Neymar wasted Dani Alves' cross minutes later, the Spanish champions regained control.
Barcelona was further helped when Filipe Luis was sent off, and Pedro appeared to have given Messi the opportunity to ensure the trophy when he earned by a foul in the box from Miranda.
But Messi struck his spot kick off the woodwork to the shock of the home fans.
Barcelona won the Super Cup - contested by the winners of the previous league and Copa del Rey - for a record 11th time.