The 34-year-old was downbeat after watching the Argentina international get stretchered from the field at Camp Nou
The Argentina international started the game on the bench and came on in the second-half, only to be stretchered from the field following a collision with opposition goalkeeper Artur, with what appeared to be a knee problem.
"Lionel Messi is undergoing some tests, but hopefully it is not anything [serious]," he told reporters after the match.
"Clearly this is the worst news of the night and hopefully he will be back with us at 100 per cent. We tried to play as we can, we tried, we made chances and it was an open game."
Midfielder Thiago Alcantara was equally concerned with the plight of his team-mate, but remains hopeful the injury is not as bad as first thought.
"It was a game in which it was clear that we wanted to win even though we went with young players," he added.
"The bad news is Leo's injury. I hope it's nothing. We are concerned, which is normal considering the state in he was in."
Messi has yet to be ruled out of Barca's Liga clash with Betis on Sunday and thanked supporters for their concern in a short Facebook message on Wednesday night.