Two suspects who were believed to have harassed and stalked the teenager were detained in connection with the crime in the Gandhi Nagar area of eastern Delhi.
The girl was found dead at her home on Thursday and initial investigations said the death was a suicide.
However, an autopsy revealed that she had been raped before being strangled, the Hindustan Times reported.
Police believe the body was burnt in an attempt to cover up the sexual assault.
Women's groups have slammed local authorities and police in India for not doing enough to curb sexual crimes in a recent string of violent attacks on women.
On the weekend, a mother and her teenage daughter were allegedly dragged out of their car and gang-raped by a group of men near Delhi.
Sex crimes and attacks on women have been the focus of much public attention in India since the gang-rape and murder of a student on a New Delhi bus in 2012.
