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.
Barcelona face a tough test away to Celtic on Tuesday in the Champions League and will be sweating on their star player.
Messi gave Barcelona a 1-0 lead with a goal in the 21st minute, but he asked coach Gerardo Martino to be substituted after making a long sprint to pressure the goalkeeper.
Messi walked off the pitch in the 29th minute, with Xavi replacing him and spent the rest of the match on the bench and watched Adriano seal the win in the second half.
Messi missed the second game of this season after bruising his left thigh and while Barcelona may be without Messi for Tuesday’s trip to Glasgow, they should have Neymar well rested after the striker did not play at the Estadios de los Juegos Mediterráneo.
Messi’s injury comes one day after he answered a judge’s questions along with his father in a tax fraud case.