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."
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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.
(Writing by Iain Rogers, editing by Justin Palmer)
