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."
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.
The game then settled down with Barca patiently probing without ever opening up a well-organised Atleti side before the break.
And Martino was quick to praise Atletico's energetic first-half performance that restricted the visitors to very few opportunities.
"It was very difficult for us to find space to receive the ball. We couldn't find space between the lines, they were very compact and it was difficult to break through.
"To fix this we need to have more movement and precision. It is not easy, but we were better in the second-half."
Despite losing Messi at half-time, Barca improved after the break as they twice went close through Alexis Sanchez and Messi's replacement Cesc Fabregas.
Neymar was next to be introduced by Martino and it didn't take the Brazilian long to net his first Barca goal as he charged in at the back post to nod home Dani Alves' hanging cross.
Valdes had to be alert to deny Villa restoring Atleti's lead moments later before Xavi fired a free-kick just over for Barca as the game became increasingly stretched.
Courtois was forced to come to Atleti's rescue once more to deny Sanchez with a brave block from point-blank range 16 minutes from time.
However, there was to be no winner on the night, meaning the tie is still very much alive heading to the Camp Nou for the second leg on Wednesday.