Pope Francis was upset to hear that two former nuns had married in a civil ceremony in Italy, Vatican Deputy Secretary of State Archbishop Angelo Becciu says.
"How much sadness on the Pope's face when I read him the news of the two married 'nuns'!" Mr Becciu tweeted on Friday.
Federica and Isabel were joined in a civil union in northern Italy last month, taking advantage of a law passed this year that offers homosexual couples legal recognition - one of the last countries in the West to do so.
The pair, who did not give their surnames, told La Repubblica on Friday that they had fallen in love while serving as missionaries in the West African country Guinea-Bissau.
Federica, 44, comes from Italy and Isabel, 40, comes from South America. They said they could have done what other nuns did and live together in a convent while hiding their relationship, but said this would have been "false".
"There are many such cases where priests or nuns hide their relationships with men or women," the pair were quoted as saying, adding that they had received no help when they left their religious order.
"We felt alone, more than that, we felt abandoned."
The Italian Bishops Conference came out firmly against the government's Civil Union bill, arguing that it undermined the status of traditional families.
The Church teaches that homosexuality is not sinful but homosexual acts are, and that homosexuals should try to be chaste.
However, Pope Francis said in June that Christians and the Roman Catholic Church should seek forgiveness from gay people for the way they had treated them.
"(Gay people) should not be discriminated against. They should be respected, accompanied pastorally," he told reporters.