The Brazilian's 66th-minute header, his first goal since moving to the La Liga champions from Santos, cancelled out David Villa's opener at the Estadio Vicente Calderon.
Villa's goal was also his first for his new club and came against his former side but Barcelona will go into the second leg on August 28 with the upper hand.
Whether Barcelona superstar Lionel Messi is available for that clash remains to be seen after he came off at half-time with a suspected hamstring injury.
It was Villa who struck with the first real chance of the game as his brilliant finish put Atletico ahead on 12 minutes.
A sweeping counter-attack led to Villa playing a clever pass out wide to Arda Turan and the Turkey international returned the ball to his 31-year-old teammate.
Just inside the area, Villa's volley was exquisitely controlled and found the bottom corner for his first goal in Atletico colours.
Barcelona characteristically controlled possession but struggled to create much against a well-drilled Atletico defence.
Making matters worse for Barca, Messi made way at half-time and was replaced by Cesc Fabregas.
The former Arsenal captain went close to an equaliser four minutes into the second half, moments after Alexis Sanchez was denied by Thibaut Courtois in a one-on-one.
After the Chilean's effort was kept out, he set up Fabregas, who was unable to get a shot away under a last-ditch tackle from Turan.
Clear-cut chances were few and far between for Barca and Andres Iniesta tried his luck from range but his effort was comfortably saved by Courtois.
Diego Costa forced Victor Valdes into a save on the hour-mark before Barcelona equalised through Neymar six minutes later.
The Brazil star had been introduced just seven minutes before he headed in a Dani Alves cross at the back post, after the right-back exchanged passes with Xavi.
Alves' cross was perfectly weighted and Courtois was unable to get across quick enough to keep the header out at his near post.
Barcelona looked the more likely to find a winner and had Xavi curl a free-kick just over on 72 minutes.
Courtois came out quickly to block a Sanchez shot at the back post minutes later as the visitors took control of the contest.
A tired-looking Atletico side were pinned back into their defensive half but they remained compact enough to keep Barcelona at bay.
