David Villa had given the hosts the perfect start when he netted against his old side in spectacular fashion after just 12 minutes.
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.
"He had a knock and then a muscle problem so we will do the required examinations to see how serious it is," Barca boss Gerardo Martino said of Messi's injury afterwards.
"It didn't make sense to keep him on the field if he couldn't move comfortably," he added.
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.
Moments later the Spanish international nearly punished his former teammates again as he and Diego Costa combined perfectly but this time Gerard Pique recovered just in time to block Villa's effort.


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