He had sustained bullet injury in the neck.
Prajapati, an Ayurvedic doctor, parted way with Asaram after an over-decade-long association when the controversial spiritual leader was accused of raping a minor girl. He also gave statements against Asaram to the police.
Prajapati had been raising his voice against Asaram since last few years.
There have been attacks on witnesses in the alleged rape cases against Asaram and his son Narayan Sai.
Asaram is lodged in Jodhpur jail since his arrest in September, 2013 for an alleged sexual assault case registered by a minor girl.
In Surat too, a woman has accused Asaram of rape and illegal confinement in his ashram. He was recently chargesheeted by the police after a SIT investigation.