The three-month-old has been handed over to her new parents, a couple from the western state of Maharashtra, child welfare officials in Chandigarh told BBC Punjabi.
The harrowing case of the 10-year-old rape victim has made headlines for weeks, both in India and globally.
Her uncles were sentenced to life in prison last month.
The second uncle was arrested after the baby's DNA sample did not match that of his older brother, the first suspect.
"The infant has been handed over to the new parents," social welfare department official Rajni Gupta told BBC Punjabi on Wednesday. "The parents were very happy," she said.
There has been a massive increase in the number of child rapes recorded in India last year, says the BBC's Geeta Pandey in Delhi.
According to the latest figures released by the National Crime Records Bureau, the number of rape cases has risen from 8,800 in 2015 to 19,920 in 2016, which is an increase of more than 100%, our correspondent says.
The 10-year-old's pregnancy was discovered in mid-July when she was taken to hospital after complaining of a stomach ache. She delivered the baby in August.
She was 30 weeks pregnant when a local court in Chandigarh turned down her abortion plea, on the grounds that her pregnancy was too advanced. A panel of doctors had advised that a medical termination would be "too risky". Later, India's Supreme Court also refused to allow her an abortion on similar grounds.
Indian law does not allow terminations after 20 weeks unless doctors certify that the mother's life is in danger.
The girl was not aware of her pregnancy, and was told her bump was caused by a stone in her stomach.
She initially told police and child welfare activists that she had been raped several times in the past seven months by the first uncle, who is in his 40s.
She had also testified to the court by video link and very clearly named the uncle and revealed details about her abuse.
The girl's father had told the BBC that the first uncle had not denied the charges against him. Police also said he had admitted to the allegations.
But after his DNA test results did not link him to the baby, police began searching for more suspects - and arrested the second uncle in September. A DNA test confirmed that he was the baby's father.
India's courts have received several petitions in recent months, many from child rape survivors, seeking permission for abortions.
In most cases, their pregnancies are discovered late because the children themselves are not aware of their condition.
In September, a 13-year-old girl was given court permission to terminate her pregnancy at 32 weeks. The boy she was carrying was born alive in Mumbai but died two days later.
In May, a similar case was reported from the northern state of Haryana where a 10-year-old, allegedly raped by her stepfather, was allowed to abort. She was about 20 weeks pregnant, doctors said.
None of the girls can be named for legal reasons.
Photo copyright: NOAH SEELAM/AFP/GETTY IMAGES. Caption: According to the latest government figures, a child is raped every 27 minutes in India