The goalkeeper didn't feature in the club's final game of the season as his coach is certain he will play again next term
The 31-year-old announced his intention to see out his contract on Friday, although he maintained he would leave Camp Nou once it expired in 2014.
Jose Pinto was handed a rare start between the posts instead, and Vilanova stated that Valdes being given a rest was not an issue as the goalkeeper will play for the club again next season.
"During the week I talked to him several times and we agreed he wouldn't play today because we were made to understand it wouldn't be his last game for us," the trainer told reporters after the match.
"What I want is for him to have the goal well covered, and I'll be happy. But if he sees another opportunity to play for another team, I'll still be happy.
"It [his future] is his decision, not mine. Victor explained sufficiently, I see the situation quite clearly. He said he has no problems staying, and so, I have no problems continuing."
Thiago Alcantara is another player who has recently been the subject of transfer speculation, but Vilanova reaffirmed his faith in the midfield starlet.
He added: "Yesterday I was wrong to say he was the club's future, because he is also the present. I have all the confidence, and so should he, in competing with the players that have been the best in the position for the past five years.
"Overall, our campaign was very good, from the first day to the last day of the league, with 100 points attained and 115 goals scored."
The Catalans equalled Real Madrid's record haul of points on the way to being crowned Spanish champions this term.