Upon his arrival at the helipad, Benedict embraced his successor before the two went to the chapel of the Apostolic Palace for a short time of prayer.
Pope Francis did away with the convention of taking the place of honour and insisted that they pray side by side, saying "We are brothers".
They then proceeded to the library where they had a private meeting that lasted around 45 minutes, before having lunch together.
The Vatican said it is was the first such meeting between a Pope and Emeritus Pope. Precise details of their conversation have not been made available but Vatican spokesman Fr Federico Lombardi said today's meeting was a "moment of profound communion".
It was also a chance, he said, for Benedict "to renew his profession of reverence and obedience".
"Certainly Pope Francis renewed his gratitude, and that of the whole Church, for Pope Benedict's ministry during his pontificate," he said.
The two have spoken on several occasions by telephone since Pope Francis' election 10 days ago but it is the first time they have met face to face.
Before his resignation last month, Benedict pledged his obedience to his successor.
The Pope Emeritus has been residing at Castel Gandolfo since his resignation and is expected to move into new accommodation within the Vatican at the end of April.