The court in Grosseto ordered the city council on Wednesday to list the couple, who had their wedding in New York in 2012, as married.
But Angelo Bagnasco, the president of the CEI, has argued that marriage should be between “a man and a woman”.
In a statement on the CEI’s website, he said the court’s decision “raised serious questions” and was likely to “sweep away the fundamental pillars of the institution of marriage” that are “rooted in our culture, and recognized and guaranteed in our constitution”
Grosseto judge Paolo Cesare Ottati ruled that there was "no reference to gender" in the city council register of married couples and the couple in question should therefore be included.
The right to marry "has acquired new and wider connotations, which include marriage between two people of the same gender," the judge said.
Gay rights activists described the move was “historic”.
"This is an unprecedented case in our country," Sergio Lo Giudice, a senator for the Democratic Party and a former head of the watchdog Arcigay, said.
Aurelio Mancuso, head of Equality Italia, said: "They have managed to achieve what has always been denied by city authorities and courts - having their status as a couple married in a foreign country recognized".
Italy is one of the few countries in Europe that does not recognize same-sex civil unions or marriage.
The couple, who are 68 and 57 years old, were denied registration following their marriage in New York in 2012 but had appealed to the court.
A local daily, Il Tirreno, named them as Giuseppe Chigiotti, an architect, and Stefano Bucci, a journalist.