As his supporters clashed with police outside, the bearded 72-year-old entered the Jodhpur Central Jail and was offered a 'chatai' or reed mat, a blanket and a mug for his prison stay.
"He is fine and is being treated as a usual prisoner," a jail official told IANS, referring to the godman who has millions of followers in India and abroad.
A medical examination was conducted on him in the jail.
Giving his ruling amid tight security, District and Sessions Judge (Rural) of Jodhpur Manoj Vyas sent Asaram Bapu to judicial custody until Sep 15.
"We have filed a bail application in the same court. The hearing is scheduled tomorrow at around 11 a.m.," Pradeep Chaudhary, an advocate for the religious leader, told IANS.
Asaram Bapu was earlier Monday quizzed at a guest house of the Rajasthan Armed Constabulary in connection with the case of sexual assault lodged against him by a 16-year-old girl, an official said.
The incident allegedly took place Aug 15 in his ashram outside Jodhpur city. The spiritual guru and his supporters have denied the charge. Police say, however, that they have a water-tight case against him.
He had been flown to Jodhpur Sunday afternoon after his arrest from his ashram in Indore in Madhya Pradesh after which he was first sent to a day's police remand.
Police questioned him Sunday evening and Monday.
His 'sevadar' (caretaker) Shiva, who surrendered to police Saturday, was also questioned. He was formally arrested Monday, a police officer told IANS.
Shiva allegedly stood outside the room where the girl was assaulted.
The officer added that Asaram Bapu claimed innocence before investigators and denied the allegation of sexual assault levelled against him.
"Asaram has cooperated in the investigation. But there are contradictions in his statements," the officer said.
As the man was brought to prison, some 400 of his supporters gathered outside shouting slogans. The protest soon turned violent, and police used batons to disperse them.
About 125 of them were detained.
The girl lodged a complaint with Delhi Police Aug 20, triggering an investigation against the influential spiritual leader who has more than once figured in the news for the wrong reasons.
Asaram Bapu's son claimed that the girl was "mentally unstable".
The spiritual leader has been booked under the Protection of Children from Sexual Offences Act and the Indian Penal Code.
According to the girl, who studied at Asaram Bapu's ashram at Chhindwara in Madhya Pradesh and stayed in a hostel there, she was sexually assaulted on the pretext of exorcism.
The girl's family, from Uttar Pradesh, was also devoted to Asaram Bapu until this alleged incident.
In the prison, the man who used to start his day eating dry fruits will now be offered 'channa' (gram) and jaggery.
Asaram Bapu has requested officials that he should be allowed to perform 'satsang' (collective prayers) in the prison every morning.
"We are considering the request as it would be a good recreation for other prisoners too," said the official.
Asaram Bapu started his first ashram on the bank of Sabarmati river in Gujarat in 1972.
Over the decades, he became a cult figure, and his public discourses attract tens of thousands of men and women across the country.
He is said to have over 425 ashrams, more than 1,400 Samitis and over 50 gurukuls.
--IANS (Posted on 02-09-2013)