Messi had to be carried off the pitch after a late collision with the opposing goalkeeper in Barcelona's 0-0 draw against Benfica in the Champions League on Wednesday.
Vilanova says Messi "feels well, he isn't bothered (by the knee). If he is traveling it's because he's in condition to play" in Sunday's match.
Forward Alexis Sanchez and defenders Dani Alves and Marc Bartra have also recovered and are in Barcelona's squad.
Barcelona leads the league after a record start of 13 wins and one draw from the opening 14 rounds.