The girl was allegedly attacked by the 45-year-old married man two months ago, reports the Indian Express.
When he turned up at the house in Northeast Delhi’s Khajuri Khas, India, he was tied to a chair, assaulted and killed, though the father denies he wanted the man to die.
He said: "I burned his genitals once, he screamed. I did it again, he shuddered. When I did it the third time..he did not move. He was dead…I did not want to kill him."
The father turned himself in to police after the incident and gave a blow-by-blow account of the incident.
A police spokesperson said: "Based on his statement, we sent a team to the spot and recovered the body. It has been sent for a post-mortem examination and his family has been informed.
"A case of murder has been registered and the 36-year-old man was arrested."
The father only found out about the original attack after he was told by doctors that his daughter was pregnant.
He decided to take action himself and not tell police to protect his daughter's honour.
The incident is not the first case of vigilante justice against alleged rapists in recent days.
Last month a man was castrated by a mob after being caught trying to rape a teenage girl.
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India has been plagued recently for a string of brutal sex attacks against women and public anger has swelled considerably following an number of high-profile cases.
Despite this, police called for those responsible for the castration to come forward.
A police spokesman said: "People cannot take the law into your own hands.
"As deplorable as these crimes are, law and order has to be maintained, and not lynch justice. We ask those men who carried out this attack to hand themselves in before we find them."