The court in Grosseto in Tuscany ordered the city council to list the couple, who had their wedding in New York in 2012, as married in a ruling that was immediately hailed by gay rights campaigners as 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, told reporters.
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".
Fabrizio Marrazzo, a spokesman for Gay Center, also hailed "a revolutionary event that deserves a positive political response" from Prime Minister Matteo Renzi.
Italy is one of the few countries in Europe that does not recognize same-sex civil unions or marriage.
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.
The two, 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.