The former Arsenal man took the brunt of the crowd's disappointment with the humiliating exit from the Champions League at the hands of Bayern Munich.
Fabregas has struggled to win over the supporters at Camp Nou since moving back to the Catalan giants, but Vilanova has strongly defended his player, insisting that he is "of great quality".
"Cesc is a player of great quality," said Vilanova.
"It was very difficult for him to come here, but last season he was our second top scorer and this season he's going the same way again.
"His performances are very good and I don't think the majority of people in the stadium the other day focused their displeasure on him. He's a big asset to the team."
Fabregas has scored 13 goals in all competitions so far this season.