The High Court's order came after two doctors who re-examined the body gave conflicting opinions.
Earlier, seven forensic experts including one chosen by Ilavarasan's family had viewed the video recording of the first autopsy. Of the seven doctors, only the one chosen by the family wanted a second autopsy.
21-year-old Ilavarasan married Divya Nagaraj, a girl from the Vanniyars, an upper-caste Hindu community, in August. Weeks after they eloped, Divya's father committed suicide which triggered riots against Dalits in and around their village. Around 250 Dalit homes were allegedly torched by Vanniyars.
Divya appeared before the court last week and said she doesn't want to return to her husband citing continuing animosity between the two communities and haunting memories of her late father. The following day, her husband was found dead near a railway track.
The first autopsy report had revealed that Ilavarasan died of a head injury. His parents, however, have alleged murder and point fingers at the dominant Vanniyar community and the PMK that backs it.
A second autopsy performed in the presence of their doctor, they hope, would find evidence that would strengthen their case.