The club said on its official Twitter account that "Messi has a muscle injury in his right thigh" and he would undergo more tests on Sunday.
Messi gave Barcelona a 1-0 lead with a goal in the 21st minute. He asked coach Gerardo Martino to be substituted eight minutes later after making a long sprint to pressure the goalkeeper.
Messi walked off the pitch, with Xavi Hernandez replacing him. He spent the rest of the match on the bench and watched Adriano seal the win in the second half.
"I hope it's nothing and he can be with us for the upcoming games because he's an important player," Adriano said. "The team is completely different with him."
Messi missed the second round of this season after bruising his left thigh. The Argentina forward missed several games at the end of last season with a right hamstring pull.
While Barcelona may be without Messi for Tuesday's trip to Glasgow to play Celtic, it should have Neymar well rested after the striker didn't play at Juegos Mediterraneos Stadium.
Messi's injury comes one day after he answered a judge's questions along with his father in a tax fraud case.