72-year-old Asaram, who was flown from Indore where he was arrested after midnight amid high drama, cleared a potency test conducted on him at the SN Medical college here.
He was also taken to the Manai ashram, 30 km from Jodhpur, where the incident was recreated to verify the charge against him, Jodhpur DCP Ajay Pal Lamba said.
Asaram was later produced before District and Sessions Judge (Rural) Manoj K Vyas who remanded him to one-day police custody. Police had sought two-day custody of Asaram.
He has been kept under police custody at the RAC Battalion campus after his plea for being allowed to stay at his ashram was rejected.
Earlier, Jodhpur Police Commissioner Biju George Joseph told reporters that there were still some issues that needed to be worked out for a "water-tight" case against Asaram.
Joseph said a medical test was carried out on Asaram and there was nothing to suggest that he was unwell. Asaram had claimed that he could not meet the deadline of August 30 given by the Jodhpur police to appear before it as his health condition had deteriorated.
Asaram has denied sexual assault charges lodged against him by the schoolgirl, the police commissioner said.
He refuted reports that Asaram was on a hunger fast and refusing to eat or drink anything. "He is taking food and water," Joseph said.
Asaram was brought by Rajasthan police team led by Additional Commissioner of Police Satish Jnagid. They were flown via Delhi in an Air India flight at about 1230 hrs.
He was taken to Rajasthan Armed Constabulary Battalion Campus in Mandore where he was interrogated for four hours, police said.
Unprecedented security arrangements were made at the airport. Asaram's supporters shouted slogans at the Delhi and Jodhpur airports.
A report from Mumbai said they also stopped trains at Ulhasnagar's railway tracks in the neighbouring Thane district shortly after noon.
Asaram was arrested by the Jodhpur Police after midnight from his ashram in Indore and escorted by a large posse of police personnel to the airport, where he spent the night on a sofa in the VIP lounge.
His arrest followed an FIR filed by the girl alleging she was sexually assaulted by Asaram at his ashram in this Rajasthan city.