The charges were framed by additional district sessions court judge H S Muliya against Sai, who is under arrest since December 2013.
The court posted further hearing for September 1. Seven persons, including Sai and his aides -- Ganga alias Dharmishtha Pramod Mishra, Jamuna alias Bhavna Madhusudan Patel, Ramesh Malhotra, Hanuman alias Kaushal Thakur, Mohit Bhojwani and Monica Agrawal were charged under IPC sections for rape, unnatural sex, molestation, wrongful confinement, unlawful assembly, criminal intimidation and criminal conspiracy.
Three others Pankaj Dewade, Ajay Diwan and Neha Diwan all Sai's aides, were charged under IPC Section 212 for harbouring an offender.
Sai, 43, was arrested for allegedly sexually assaulting the victim repeatedly during her stay as an inmate at his ashram here between 2002 and 2005.
He was arrested from near the Delhi-Haryana border in December 2013 after evading law for two months following registration of the case against him.
The victim's elder sister had also made similar allegation against Sai's father Asaram while she was living at an ashram in outskirts of Ahmedabad between 1997 and 2006.
The two sisters had lodged separate complaints against Sai and Asaram for allegedly raping them. Other accomplices of Sai were also arrested later for aiding and abetting him in various offences.
Earlier in June, charges were framed against Sai and 10 others in another case of hatching a conspiracy to bribe police and judicial officials to weaken the rape case against him.