The 32-year-old midfielder was unable to complete Thursday's game as he was replaced by Andre Gomes at half-time
Andres Iniesta suffered a calf injury in Barcelona's Copa del Rey victory over Real Sociedad.
Barca confirmed after the first leg of the quarter-final tie that the midfielder had suffered the problem to his left calf and will undergo medical tests on Friday.
Iniesta, 32, had been replaced by Andre Gomes at half-time, the latest blow in a season that has been interrupted by two knee injuries.
The match itself saw Luis Enrique's holders win 1-0, ending their curse at the Anoeta with a first win in nine attempts courtesy of Neymar's first-half penalty, delighting Sergio Busquets.