The brief meeting – just under half an hour at the Vatican – was the latest stop for the royal couple on a charm offensive that started in Romania last week and ends in Austria on Wednesday.
It also follows a visit by Charles's son Prince William and his wife Kate to Paris in March.
At the Vatican, Charles presented the 80-year-old pontiff with a collection of products from his Highgrove estate, where the prince indulges his passion for organic farming.
“It's difficult to know what to give to your holiness,” he said.
“It may come in handy or somebody else might like it – it's all homemade things I produced.”
Camilla then chipped in: “It's very good.”
The pope gave the couple a bronze of an olive branch, telling the prince, “Wherever you may go, may you be a man of peace.”
Charles replied: “I'll do my best!”
The pope also gave them copies of the three major texts he has produced since becoming pope just over four years ago.Laughing, Charles asked: “Are they in English?”
When the pope confirmed they were, he added: “You are very generous – a great treat.”
The Italian leg of the royal tour has been widely seen as a success, with Charles praised in the Italian media for visiting earthquake-devastated Amatrice on Sunday and announcing plans for a food-related scheme to raise money for the victims.
IN PICTURES: Prince Charles in Italy's earthquake-damaged towns
Camilla also attracted favourable coverage for her various visits, including one without her husband to an NGO helping the victims of human trafficking.
She also won over the locals in Florence by recalling her childhood ties to the city, where the visit began with a sundown stroll over the Ponte Vecchio on Friday.
The couple also helped celebrate the 100th anniversary of the British Institute in Florence, where Charles was honoured as “Renaissance Man of the Year” on Monday.
Camilla, the Duchess of Cornwall, wore a gold-coloured silk coat and dress that contrasted with the traditional black outfit complete with veil that she wore when she and her husband met Francis' more traditionalist predecessor Benedict XVI, in 2009.
Charles's first wife, the late Diana, Princess of Wales, also wore black on her two visits to the Vatican, but Francis has let it be known that he does not expect sombre garb on his female visitors, in line with his efforts to project an image of an unstuffy Church that is not obsessed with rules.
Charles opted for an appropriately royal shade of blue for his discreetly checked suit, which was paired with a polka-dot tie.
The couple had earlier visited The British School, a Rome institute for the study of the ancient city and modern Italian, which is housed in a building designed by renowned British architect Edwin Lutyens.