Messi, who scored Barca's opening goal from the penalty spot, was replaced by Arda Turan at halftime at the Nou Camp and Luis Enrique told a news conference he had taken the decision as a precaution.
The Argentina forward and FIFA Ballon d'Or holder missed two months late last year with a knee injury but has looked close to his best in recent weeks.
"Tomorrow tests will be conducted, he has some mild muscle fatigue," Luis Enrique told a news conference.
"There was no sense in taking risks," added the former Barca and Spain midfielder. "I don't like to risk anyone, least of all Messi."
Barca's Spain fullback Jordi Alba also had to come off in the second half after sustaining what looked like a hamstring strain when lunging for the ball.
Second-placed Barca, who are two points behind leaders Atletico Madrid with a game in hand, play at Bilbao in the first leg of their King's Cup quarter-final on Wednesday.
Barca beat Bilbao 3-1 in last year's final and the return is at the Nou Camp a week later.
REUTERS