Fabregas bagged a brace while his Spain international teammate scored the winner in injury time in the Blaugrana's 3-2 away win.
"Villa is absolutely vital," said Vilanova. "He has an important knack for scoring these types of goals.
"It was the reason behind my idea to deploy him as centre-forward. After just a month of being back in action, it couldn't have gone any better for him. The 3-4-3 formation has proven vital in helping Villa leave his mark.
"Meanwhile, Cesc, has run a lot and played at a very high level, always reflecting the desire I harbour for the team to play and win. He has shown he is feeling better and better."
Barca's victory at Estadio Ramon Sanchez Pizjuan sees them maintain their perfect start to the league campaign with six wins out of six.