Barca said in a statement: "The club expresses their deepest condolences over the passing of Tito Vilanova, who died today in Barcelona at the age of 45."
Vilanova, a former midfielder who spent his playing career largely in the Spanish second division, was diagnosed with cancer of the salivary gland more than two years ago and was forced to step down as Barca boss last July.
He was Pep Guardiola's assistant during a glorious four-year spell for Barcelona between 2008 and 2012 during which the club won 14 trophies.
Vilanova took over from Guardiola at the start of the 2012/13 season, but he had to take four months off between December 2012 and April 2013 for treatment in the United States after a recurrence of the throat cancer which had been first diagnosed in November 2011.
Barca went on to win the Spanish La Liga title, equalling the record points tally of 100, in his only season in charge before he finally resigned because of ill health.
Vilanova, who was admitted to a hospital in Barcelona last week, is survived by his wife, Montse Chaure, and two children. His son Adrian is currently in Barcelona's youth academy.
Barca sent their "deepest condolences" to Vilanova's family and said they would be opening a space in the main grandstand at the Nou Camp for people to express their condolences.
The club's president Josep Maria Bartomeu said on Twitter: "Tito Vilanova was a wonderful person, and will never be forgotten at FC Barcelona. Thank you for everything you taught us. Rest in peace."
Barca star Lionel Messi and midfielder Cesc Fabregas both paid emotional tributes on their Facebook pages.
Messi wrote: "A person difficult to forget. I will always remember you. All my love to the family of Tito."
Fabregas wrote: "Tito, thank you for all you have given to football and Barca.
"Personally, I met you 14 years ago and I can say that there are very few people like you. Thank you for always trusting me to help me improve and overcome personal and professional obstacles.
"We will always keep a place for you in our hearts. Rest in peace Tito."
Florentino Perez, the president of Barca's great rivals Real Madrid, also paid tribute to Vilanova on behalf of his club.
"I want to express my deep sorrow at the death of Tito Vilanova and transmit, on behalf of Real Madrid, our condolences, love and support to his family, to FC Barcelona and most especially his wife and children," he said in a statement.
"Today is a day of great sadness for all football fans and recognition of his personal and professional career. "
Chelsea boss Jose Mourinho had several run-ins with Vilanova during his time in charge of Madrid, infamously poking him in the eye in one clash.
Mourinho said on Chelsea's Twitter account: "Tito Vilanova's passing is a sad day for football, for Barcelona and most importantly for his family and friends.
"On behalf of everybody at Chelsea Football Club I send my deepest condolences at this most difficult time."
Madrid defender Sergio Ramos added on Twitter: "Lots of support to all of Tito's family and friends. An example of fighting and strength for all of us. RIP."
Madrid's former player Michel Salgado played alongside Vilanova for Celta Vigo, where Vilanova spent three seasons from 1992 to 1995.
"Destroyed over Tito Vilanova's death, my condolences to family and friends and such a big honour having played with him in Celta," he said.