The club announced that the operation on Vilanova's parotid gland had gone 'as expected' and that he would be spending the next six weeks undergoing chemotherapy.
Vilanova also had a tumour removed from his throat in November last year when he was Pep Guardiola's assistant.
His own assistant coach, Jordi Roura, will be in charge of the team for Saturday's Spanish league game at Valladolid.
A club statement read: "Vilanova's surgical procedure has gone as expected. His clinical progress will determine how long he remains in hospital.
"The expected timeframe has been maintained. Tito asks for his privacy and confidentiality to be respected."
Club captain Carles Puyol added: "The first message I have received is that the operation has gone very well but it is very tough news, a very hard blow."
And Barcelona president Sandro Rosell said: "We will have to try to go on as normally as possible but there will not be total normality because Tito is the coach and now for a few weeks he will not be there. Tito is very strong and we are convinced he will come back to us soon."