The Marussia driver, who had been tipped as a likely future star with every chance of racing for Ferrari, had been in a coma since the accident at Suzuka.
He was the sport's first driver fatality as the result of race injuries since Brazilian triple world champion Ayrton Senna and Austrian Roland Ratzenberger died at the San Marino Grand Prix at Imola in 1994.
Hundreds of fans gathered outside the cathedral, where large portraits of Bianchi in racing overalls were displayed above floral tributes, and applauded the late driver as the coffin was carried in by his peers.
His helmet was placed on top.