The two met for about 50 minutes and agreed on the need to recreate a climate of dialogue in Ukraine and to implement a peace deal designed to end fighting between Ukrainian government forces and pro-Russian separatist rebels, the Vatican said.
The meeting underlined how Francis has been increasingly using his role for diplomatic ends - particularly following the deal he brokered last year between Cuba and the United States to resume diplomatic relations after more than half a century.
Putin, who has been shunned by the Group of Seven nations over Russia's annexation of Ukraine's Crimea region last year, was received with full honors and regalia at the Vatican, including a ceremonial Swiss Guard welcome.
But the Argentine pope, who is usually chatty with world leaders when they enter his study, seemed stiff and exceptionally formal when he greeted Putin with a curt "willkommen" (welcome) in German. Both men remained silent until reporters were ushered out.
The tone of the Vatican statement after Wednesday's meeting also suggested Francis had been blunt with Putin behind closed doors. The word "cordial," which is used in nearly every Vatican statement about the pope's talks with a world leader, did not appear.
Earlier on Wednesday, the U.S. ambassador to the Vatican, Ken Hackett, urged it to criticize Russia's involvement in the Ukraine conflict more forcefully.
"It does seem that Russia is supporting the insurgents and does seem that there are Russian troops inside Ukraine," Hackett said.
Moscow has dismissed Western accusations that it is arming the separatists in eastern Ukraine and sending its own soldiers to join the fight.
Kremlin spokesman Dmitry Peskov told reporters Hackett's words were an "unacceptable" attempt to influence the sovereignty of other countries.
The Vatican said the pope told Putin that it was essential to resolve the "grave humanitarian situation" in Ukraine, allow aid into conflict areas, and work for "progressive detente in the region".
Francis warmed up a bit during a picture-taking and gift exchange session after their private talks, speaking to Putin within earshot of reporters of the need for a "peace that overcomes all wars" and "solidarity among peoples".
Putin met the pope after holding talks with Italian Prime Minister Matteo Renzi in Milan where the Italian leader showed little sign of breaking ranks over European Union sanctions on Russia in response to Moscow's role in Ukraine.