Seven other accused were acquitted by the court. One accused died during the course of the trial, which was shifted to Mumbai from Gujarat.
The quantum of sentence will be pronounced on Monday.
Bilkis, who was six months pregnant, was gang-raped during the communal violence that erupted in Gujarat after a coach of Sabarmati Express carrying Ramsevaks from Ayodhya was set on fire on February 27, 2002.
Bilkis was also a prime witness to the murder and rape of members of her family and community during the riots.