The law student was at her residence in the state capital Thiruvananthapuram late Friday when she says she was attacked by the 54-year-old man, who had claimed to her family to be a religious guru.
"She used a knife in her defense and cut off his penis," district police chief G Sparjan Kumar told AFP by phone.
"The man, Hari Swami, was rushed to the nearby government hospital in a serious state," he added.
Local media reports that Swami was in a stable condition after undergoing emergency medical procedures.
The woman claimed he had been assaulting her for several years, according to Kumar, who said police had registered a case against Swami for sexual offences against a minor and rape.
Police said the girl's parents, who live at the same house, were unaware of the assaults by Swami, the Daily Mail reported.
"The woman told us that her parents blindly trusted this Swami, and he used to get frequent invites to perform special ceremonies and stay over at their house, where he assaulted her," Kumar told AFP.
She is now under police protection and receiving trauma counselling.