David Villa had given the hosts the perfect start when he netted against his old side in spectacular fashion after just 12 minutes yesterday.
Barca then struggled to find their rhythm against a dogged Atleti side and were dealt a huge blow when Messi failed to reappear for the second-half due to a hamstring injury.
However, in his absence, Neymar was the man to rescue the Spanish champions as he came off the bench to head home Dani Alves' cross 25 minutes from time.
"It didn't make sense to keep him on the field if he couldn't move comfortably."
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Having thrashed Levante 7-0 Martino's first competitive match in charge on Sunday, Barca started confidently and had the first clear opening of the game when Pedro's scuffed effort was palmed away by Thibaut Courtois on 11 minutes.
Within 60 seconds though Atleti were ahead though thanks to a fantastic piece of counter-attacking play as Villa fed Arda Turan on the left then burst into the box to meet the Turk's cross flush on the volley to power the ball past Victor Valdes.