Sai was produced before the court of Chief Judicial Magistrate Jatin Thakkar by police following expiry of his 14-day judicial remand.
The 42-year-old son of Asaram is accused of repeatedly sexually assaulting one of the two sisters, who was the inmate of his ashram here, between 2002 and 2005.
It was during Sai's earlier remand period (in connection with the rape case) that the city crime branch had unearthed a plan to bribe cops, doctors and even judicial officers to dilute the rape case.
Sai was arrested from Delhi-Haryana border in December last after evading law for nearly two months following registration of the rape case against him.
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Two sisters had lodged complaints against Sai and his father accusing them of rape, sexual assault, illegal confinement and other charges.
Surat Police had booked Sai under various IPC sections including rape, unnatural sex, molestation, wrongful confinement, unlawful assembly, rioting armed with deadly weapon, criminal intimidation and criminal conspiracy.
In her complaint, the younger of the two had accused Sai of repeated sexual assault between 2002 and 2005 when she was living at the Surat ashram.
Asaram (72) is currently lodged in a Jodhpur jail in connection with alleged sexual assault of a minor daughter of one of his followers at his Jodhpur ashram last year.
A chargesheet was filed against him last month in a court in Gandhinagar.