Sources said Asaram has been taken to the Indore airport, from where he will be flown to Jodhpur for interrogation. The arrest came at the end of a day marked by Asaram's defiance as the police team tried to interrogate him.
The victim's father, who had started a hunger strike in Shahajahanpur in Uttar Pradesh demanding Asaram's arrest, has reportedly ended his fast.
Earlier on Saturday, Asaram's son Narayan Sai had claimed his father was unwell and could not be interrogated.
A senior Rajasthan cop later countered the claim, saying the 72-year-old self-styled godman is medically fit to be investigated and could be arrested if they are not satisfied with his defence against the allegations made by the teenage inmate of his ashram.
The 16-year-old girl had lodged a complaint with police on August 20, accusing Asaram of sexually assaulting her at his Jodhpur ashram.
Asaram had denied the charges with his son saying that the girl was "mentally unstable". He had also blamed Congress president Sonia Gandhi and her son Rahul Gandhi for his predicament.
There was tension in Jodhpur on Saturday with Asaram's supporters attacking the journalists at his ashram, which has now been sealed. Thirteen people were detained for the violence.
"Asaram Bapu's supporters snatched our mikes and camera," said a TV journalist who was hit on his head. Another journalist received stitches after he was wounded.
Asaram's associate and bodyguard Shiva, who is accused of taking the girl to the guru's Jodhpur ashram, surrendered to the police earlier on Saturday.
Last December, the self-styled godman had made the controversial remarks that the Delhi gang-rape victim may have been spared if she had addressed her attackers as brothers.