The papal Almoner's Office announced on Sunday that two Christian families and one Muslim family have already moved into apartments in the city.
The papal office added that the Christian families had suffered "kidnapping and discrimination" because of their faith while in Syria.
"The mother [of one family] had been kidnapped for several months by ISIS and now, in Italy, has regained serenity," the office told Catholic News Service.
Pope Francis first appealed for the Vatican to take in refugee families in September 2015.
At the time, the pontiff called on "Every parish, every religious community, every monastery, every sanctuary of Europe, take in one family" in order to combat the refugee crisis.
The Vatican then took in three families who Pope Francis brought from Italy after a visit to a refugee camp on the Greek island of Lesbos, as well as nine more refugees who arrived later.
The nine have now started new lives elsewhere in Italy with the support of the Vatican.