"How much sadness on the Pope's face when I read him the news of the two married 'nuns'!" Becciu tweeted.
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 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."