A humanitarian decision to abort to save the life of a raped nine-year-old girl only led to the excommunication of the child's mother and the doctors.
While the Brazilian church's move has triggered fierce criticism across the globe, the Vatican itself strongly defended the decision of the archbishop.
Cardinal Giovanni Battista Re, head of the Catholic church's Congregation for Bishops, told the daily La Stampa on Saturday declared the twins the girl had been carrying were precious and they had a right to live.
"It is a sad case but the real problem is that the twins conceived were two innocent persons, who had the right to live and could not be eliminated," he said in an interview.
Re, who also heads the Pontifical Commission for Latin America, added: "Life must always be protected, the attack on the Brazilian church is unjustified."
Abortion is illegal in predominantly Catholic Brazil, but the law admits exceptions in cases of rape or if the mother's life is at risk.
The girl was 15 weeks pregnant with twins and doctors said her life was in danger. She weighed just 36kg and was 1.33m tall. The girl, whose identity was not made public, had recovered and was released from hospital on Friday.
The stepfather, 23, confessed to the rape and was arrested last week in Recife, the capital of the state of Pernambuco. According to police, the girl had been sexually abused since she was six. He is also suspected of abusing the girl's physically handicapped 14-year-old sister.
Brazilian President Luiz Inacio "Lula" da Silva on Friday said it was "regrettable" that a Roman Catholic archbishop excommunicated the mother of a nine-year-old girl who had an abortion after being raped by her stepfather.
"As a Christian and a Catholic, I deeply regret that a bishop has had such conservative behavior," Lula told reporters in the city of Vitoria.
He praised the doctors in the northeastern Brazilian city of Recife for their decision to perform the abortion.
"In this case, medicine is more right than the Church," Lula said.
Archbishop Jose Gomes Sobrinho also excommunicated the doctors who performed the procedure.
He defended his decision in an interview published on Friday by Brazilian daily O Estado de Sao Paulo.
Abortion "is a silent Holocaust," he said.
Asked why he did not excommunicate the stepfather who sexually abused the girl, Gomes Sobrinho said: "He committed an extremely serious crime. But that crime, according to canon law, is not punished with automatic excommunication."
"Abortion is even more serious. The Church and the whole world condemn the Holocaust that killed 6 million Jews. What is happening [with abortion] is a silent Holocaust," he said.
One of the doctors involved in the abortion, Rivaldo Albuquerque, told Globo television that he would keep going to mass, regardless of the archbishop's order.
"The people want a church full of forgiveness, love and mercy," he said.
Health Minister Jose Gomes Temporao also slammed the archbishop.