Hansi Flick opted to send on Pedri in his place at half-time, with the scores level at 0-0 after the first half in the Basque Country.
According to ESPN, the change was not solely a tactical substitution but because Bernal was suffering from stomach problems during the game.
Flick was quizzed on Bernal afterwards in his post-match press conference and said: “We had to sub out Marc Bernal due to a precaution. He had some discomfort.”
Barcelona will be hoping that Bernal is passed fit to play against Newcastle in midweek in the Champions League last 16 tie.