Earlier, it was suspected that her elder uncle had fathered the baby who was delivered in August this year, they said.
The sordid revelation emerged on the basis of a fresh DNA report, the police officials said adding that the minor's elder uncle too had allegedly her and was arrested.
The girl's elder uncle's DNA sample did not match that of the newborn following which the suspicion fell on his younger brother who too had been accused of rape by the victim, they said.
She maintained that both the girl's uncles had sexually exploited her.
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"A supplementary charge sheet has been filed before the court of Additional District and Sessions Judge, Poonam R Joshi, here today," the police officer said.
The rape victim, whose abortion plea was turned down by the Supreme Court, had in August delivered a baby through C- section at a government hospital here.
The child was told by her family and the doctors that she had a stone in her stomach that had to be removed. Earlier, police had said the girl was repeatedly raped allegedly by her elder maternal uncle for several months.
On July 28, the Supreme Court had dismissed a plea seeking its nod for terminating the 32-week-old pregnancy of the rape survivor after taking note of a medical report that abortion was neither good for the girl nor for the foetus.
The Supreme Court bench had taken note of the report of the medical board set up by Post-Graduate Institute of Medical Education and Research, Chandigarh, which was set up on the directions of the apex court, to examine the rape survivor and the consequences if the termination of pregnancy was allowed.
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