The girl, who was allowed by the Supreme Court to terminate her 32-week-old pregnancy on medical grounds, had on Friday delivered the baby after a caesarean section operation at the hospital, a doctor had earlier said.
The baby, who weighed 1.8kg, died on Sunday at around 10.30 am.
The premature infant was kept in the Neonatal Intensive Care Unit of the J J Hospital as most of his organs were underdeveloped, hospital sources said.
His condition turned critical and doctors removed him from an oxygen machine and put him on a ventilator, they said.
A medical officer said the hospital could not comment on the cause of the death as the postmortem report was yet to be finalised.
The teenager, who is still in the hospital, is being treated by gynaecologist Ashok Anand.
"We will discharge her from the hospital after her recovery," Dr Anand said.
In its ruling on September 6, a bench headed by Chief Justice Dipak Misra had directed that the medical procedure be conducted on the girl at the earliest, preferably on September 8, after it took note of the report of the Supreme Court-appointed medical board comprising doctors of the J J Hospital.
The victim, a Mumbai resident and a Class 7 student, had to knock the doors of the apex court as the law prohibits the abortion of a foetus after 20 weeks of pregnancy.
The bench also took note of the risk factors and asked the hospital to admit the girl a day before the abortion.
Section 3(2)(b) of the Medical Termination of Pregnancy Act prohibits the abortion of a foetus after 20 weeks of pregnancy.
The doctors at the J J Hospital said the girl's family members, who initially wanted the girl's pregnancy to be terminated, later changed their mind and were thinking of keeping the baby.
The girl was allegedly raped by her father's associate. Last month, the family discovered that she was pregnant.
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