The Argentine attacker was stretchered off in the closing stages of Barcelona's scoreless Champions League draw against Benfica, and some suspected that the prolific forward had picked up a serious injury.
However, tests have since revealed that Messi has sustained a contusion on his left knee, and although the attacker has yet to undergo further examination, Vilanova has reacted relieved.
"It looks like it’s just a knock but they will be doing more tests to rule out other possibilities," Vilanova told reporters.
"Messi was a bit worried initially, which is normal when you don't know what it is. After the first tests by the doctors, he was calm, though."
Vilanova then went on to stress that he doesn't regret his decision to let Messi come off the bench for the final 30 minutes as they had previously agreed the Argentine would make a substitute cameo.
"We talked about the possibility of him playing for 30 minutes. He’s a player who likes to play. It was part of his physical training program," the head coach continued.
"We should not take him off every time we’re leading 3-0 lest he picks up an injury. We’ve never behaved this way. If I had to repeat the game, I’d make the same decision seeing as he can get injured at any moment."
The club's sporting director, Andoni Zubizarreta, admitted that the Benfica clash was far from ideal for Barcelona, and revealed his concern over Messi being forced to withdraw with an injury.
"It was a difficult game difficult to play. We're already qualified, and considering the accumulation of matches, the cold temperature, and the wind ... It was one very unpleasant day to play," he told Canal+.
"I do not know what injury [Messi] has, but it's never nice to leave the field on a stretcher."