Their private talks lasted 55 minutes, said the Vatican, but, as is customary, it was not specified what they discussed.
Before Mr Macron's visit, they urged him to raise the issue directly with the pope.
The Vatican said that Ukraine, particularly the humanitarian situation there, topped the agenda in later talks Mr Macron had with the Vatican's two top diplomats. They also discussed the Caucasus, the Middle East and Africa.
Topics in such meetings often mirror what is discussed in leaders' private papal audiences.
Mr Macron, accompanied by his wife Brigitte and greeted with an honour guard of Swiss Guards, gave the pope a first edition of German philosopher Immanuel Kant's Perpetual Peace, published in French in 1796.
The pope gave Mr Macron a medallion depicting an early plan for St Peter's Basilica and some of his writings.
From the Vatican, Mr Macron went to an official lunch hosted by Italy's President Sergio Mattarella, having held talks with new pope Giorgia Meloni on Sunday.
Mr Macron is in Italy to attend an international conference organised by the Sant'Egidio Community, a worldwide peace and charity group. He and the pope will jointly close the conference at Rome's Colosseum on Tuesday.
Opening it on Sunday, Mr Macron said he believed there was a chance for peace in Ukraine.
He also said the Russian Orthodox Church was allowing itself to be manipulated by Moscow to justify the war in Ukraine and urged it to resist such pressure.