Asaram, 72, was brought to the city on Monday evening on a transit remand from a court in Jodhpur where he was lodged in a jail since August in another sexual assault case involving minor daughter of one of his devotees.
A magisterial court in Gandhinagar on Tuesday remanded him in four-day police custody.
Surat police recently registered two complaints - one against Asaram and another against Narayan Sai - of rape, sexual assault, illegal confinement and other charges as alleged by the two sisters.
The elder of the sisters, in her complaint, had accused Asaram of repeated sexual assault between 1997 and 2006 when she had been living in his ashram on the outskirts of Ahmedabad city. The case against Asaram was transferred to Chandkheda police station as the incident took place here.
The younger of the two sisters had filed a complaint against Narayan Sai, whose whereabouts are still not known, accusing him of repeated sexual assault between 2002 and 2005 when she was living in their Surat ashram.
Narayan Sai and Asaram had also filed petitions in the Gujarat High Court, seeking quashing of the plaints on the grounds of delay in filing them and that they are based on flimsy grounds.