The Brazilian striker netted in the 21st minute after he was fouled in the area and took the spot-kick himself.
Barca had all their first-choice attackers on the pitch but could not add to the scoreline in a low-action affair at Estadio Anoeta.
Luis Enrique’s side controlled the possession and made most of the inroads but could not find a second away-goal. They will look to finish off the job at the Nou Camp in the second leg.
In Thursday night’s other quarter-final clash Atletico Madrid eased past Eibar 3-0 at the Vicente Calderon thanks to goals from Antoine Griezmann, Angel Correa and Kevin Gameiro.