"The law of God is above any human law," the archbishop told the Globo newspaper on Thursday.
Abortion is illegal in Brazil, a strongly Catholic nation, although exceptions are allowed in cases of rape and when the mother's life could be endangered.
Girl 'in danger'
Doctors said the girl was 15 weeks pregnant with twins when the abortion was
Health officials said the girl's life had been in danger.
"As doctors, we could not allow a girl of nine to suffer like this or until she paid with her own life," Olimpio Moraes, one of the doctors involved in the abortion, told the Reuters news agency.
The pregnancy was discovered last week when the girl complained of pain and was taken to a clinic.
Police said the her stepfather had been arrested and had admitted sexually abusing the girl from the age of six, local news websites reported.
Abortion remains a contentious issue in Latin America, and debate in Brazil over the controversy grew after a second young girl, aged 11, was revealed to have become pregnant following alleged sexual abuse by adoptive father, although she is expected to keep the baby.