As for the doctors, there was no clear case that they should be expelled from the church either, he said contrary to the position taken by archbishop Jose Cardoso Sobrinho, who last week announced the excommunications.
Barbosa said only doctors who "systematically" conduct abortions are thrown out of the Roman Catholic Chuch.
The case of the young girl, allegedly raped by her stepfather in the Brazilian state of Pernambuco, has sparked a firestorm in Brazil.
Sobrinho’s position that the abortion "was more serious" than the rape prompted much public debate, with many denouncing his lack of compassion.
But the archbishop had support in principle from the Vatican.
Cardinal Giovanni Battista Re, the head of the Roman Catholic Church's Congregation for Bishops, told the Italian daily La Stampa the twins had had a right to live and that the attacks on Sobrinho were "unjustified."
In an effort to mitigate Sobrinho's declarations, CNBB president Geraldo Lyra Rocha said his colleague had been misinterpreted.
"Archbishop Sobrinho did not excommunicate anyone. I am sure he did not mean to harm anyone but rather wanted to draw attention to a certain permissiveness" over abortions, he said.
Abortion is illegal in Brazil except in cases of rape or if the woman's health is in danger.
But a million women still seek clandestine abortions in operations that kill thousands each year, according to officials.
The girl, who was not identified because she is a minor, was found to be four months' pregnant after being taken to a hospital suffering stomach pains.
Officials said she told them she had been abused by her stepfather since the age of six. Police said the 23-year-old stepfather also allegedly sexually abused the girl's physically handicapped 14-year-old sister.
He was arrested a week ago and is being kept in protective custody. If convicted, he faces up to 15 years in prison.
Image of a church in Brazil, from www.ouro-preto.info.