Pope Benedict's first big political clash since his election a year ago dimmed hopes for any re-establishment soon of official ties between the Roman Catholic establishment and Beijing that ended after communists took control of China in 1949.
Also automatically excommunicated for defying the pope were the bishops who performed the ordinations in separate ceremonies since Sunday, according to a provision of church law cited by Joaquin Navarro-Valls, the Vatican spokesman.
Benedict learnt about the ordinations "with great sadness", said Navarro-Valls on Thursday.
"It is a great wound to the unity of the church," he said.
The Vatican said that according to its information, "bishops and priests have been subjected, by institutions outside the church, to strong pressures and threats, in order for them to take part in the ordinations that, because they were not approved by the Vatican, are illegitimate and go against their conscience".
Great inner suffering
Navarro-Valls said that some prelates refused, while some others "could not do anything else but submit ... with great inner suffering".
"We are therefore faced with a grave violation of religious freedom," he said, adding that the Vatican "had thought and had hoped that such deplorable episodes belonged to the past".
Despite the harsh words on Thursday, the Vatican was leaving the door open to "honest and constructive dialogue with the competent Chinese authorities to find solutions that would satisfy the legitimate requirements of both sides", according to Navarro-Valls.
But he said that the ordination of bishops "not only does not favour this dialogue, but instead creates new obstacles".
Formal ties between Beijing and the Holy See would give Vatican loyalists in China some security.
In the last high-profile excommunication, the Vatican excommunicated seven women in 2002 - including the wife of a former governor of the US state of Ohio, as well as women from Austria and Germany - who had participated in an ordination ceremony on a boat travelling Europe's Danube River and called themselves priests.
The case was handled by Cardinal Joseph Ratzinger, who was the head of the Vatican's Congregation for the Doctrine of the Faith before becoming pope last year.