During the 40-minute meeting, the two sides brought about common spiritual values and highlighted the good state of relations between the Holy See and Iran.
The pontiff called for Iran’s help to find political solutions to ongoing problems in the Middle East, according to news agencies.
Rouhani and the Pope also highlighted the importance of interreligious dialogue and the responsibility of religious communities in promoting reconciliation, tolerance and peace.
Rouhani also presented the pontiff with a handwoven Persian carpet along with a book of illustrations by renowned Iranian painter Mahmoud Farshchian.
The meeting between the Pope and President Rouhani is the first of its kind since 1999.
Rouhani arrived in Rome on Monday at the head of a delegation of more than 100 businessmen and ministers on the first leg of his trip to three European destinations.
He will head for Paris on Wednesday to hold talks with senior French officials.