The Gandhinagar court rejected Asaram's bail plea on the grounds that the investigation in the case lodged against him is at a "crucial juncture" and the allegations against him are of "serious nature."
Recently, the Surat police registered two complaints - one against Asaram and another against his son Narayan Sai - for rape, sexual assault, illegal confinement and other charges, as alleged by the two sisters.
In her complaint, the elder of the two sisters accused Asaram of repeated sexual assault between 1997 and 2006 during the time she lived in his ashram on the outskirts of Ahmedabad city.
72-year-old Asaram was brought to the city earlier this month on a transit remand from a Jodhpur court, where he was lodged in a jail since August, in another sexual assault case.
He was grilled by Special Investigation Team (SIT) set up by city police commissioner to probe the complaint against him. Last week, he was taken back to Jodhpur.
His son, Narayan Sai, against whom the younger of the two sisters has registered a complaint of sexual assault, is absconding and Surat police are searching for him across the country.