The royal couple were greeted by an honour guard of the Swiss Guards and a Vatican nobleman before meeting the Pope for the first time.
The Prince and Camilla, who was wearing a black dress, emerged from a convoy of cars inside a courtyard in the Catholic city.
The visit to the Vatican takes on added significance following the recent announcement by Prime Minister Gordon Brown that he has been in talks with Buckingham Palace about reversing a ban on heirs to the throne marrying Catholics.