Latest from athletic bilbao
- Athletic, who knocked out Barcelona in the previous round, ended a run of three successive defeats by Real in all competitions over the last two months thanks to Berenguer's last-gasp goal.
Bilbao set up a showpiece clash on Sunday against Real Madrid, who beat Barcelona 3-2on Wednesday.
Barca's statement did not give any indication when Pique would return, stating that he would continue to be assessed.
Messi's two goals came after Antoine Griezmann finally beat Bilbao goalkeeper Unai Simón with the opener on the hour-mark.
Messi could be suspended for up to 12 games for the red card he received in the final minutes of his team's 3-2 loss to Athletic Bilbao in Seville on Sunday.