The woman had given the baby up shortly after her birth in 2011 because she wanted to stay with the "Little Sisters of Nazareth" congregation, but that request was turned down and so she asked for her baby back.
The little girl was being adopted by an Italian couple and another court had argued the nun no longer had rights as a mother because she only recognised her parenthood three and a half months after the birth.
The 44-year-old became a nun in 1996 and studied at a pontifical university in Rome, the reports said.
She said she was raped by a priest also from Democratic Republic of Congo in the city of Pesaro in central Italy in 2010 but never revealed his identity.
"The initial rejection, given the particular psychological situation of the nun, cannot allow the loss of parenthood rights," the court ruled.
A lawyer for the now former nun, Giovanni Giardini, said the situation was "very complex" but she would now "start getting to know" a daughter she has never known.
Giardini said the birth had been for her "like a death and a re-birth: a mourning for the loss of her previous life and her re-birth as a mother."