Prakash was a cook at a hostel of the ashram run by Asaram in Madhya Pradesh's Chhindwara where the girl stayed and studied, while Sharad Chandra was in-charge of the hostel.
"Prakash and Sharad were accused of being involved in the conspiracy of the sexual assault on the 16-year-old girl at Asaram's ashram near Jodhpur Aug 15. They were being searched for," a police officer told IANS.
Both had earlier filed for anticipatory bail claiming innocence, but they withdrew the application Thursday.
The officer said Prakash and Sharad appeared in the court of district and sessions judge Friday and surrendered.
"After their surrender today (Friday), they have been placed in police custody. They will be questioned by the police," said the officer.
The girl's family, from Uttar Pradesh, were followers of Aaram Bapu at the time of the incident, police said.
Asaram has been booked under various sections of the Protection of Children from Sexual Offences Act and the Indian Penal Code. He has denied the allegations.
The spiritual guru was arrested from Indore in Madhya Pradesh Sep 1 and brought to Rajasthan and is currently lodged in the Jodhpur Central Jail.
His close aide Shiva has also been arrested for abetting the crime.
Another accused, Chhindwara's hostel warden, Shilpi, had filed for anticipatory bail which was rejected by a court.
The police is still looking for her.