"In order to stop the bloodshed in Syria, we call for an immediate cessation of all violence," the leaders said in a joint statement, after meeting in Mexico following days of antagonism between Moscow and Washington on the issue.
"We are united in the belief that the Syrian people should have the opportunity to independently and democratically choose their own future."
Putin told reporters after meeting Obama for the first time since he returned to the presidency that the two leaders had found "many common points" on Syria, where violence is spiralling into an all-out civil war.
Washington has become increasingly frustrated over Moscow's refusal to allow the UN Security Council to take firmer action against President Bashar al-Assad over his brutal crackdown on civilians.
Obama said after the two hours of talks that both he and Putin agreed on the need for a "political process" to prevent civil war in Syria and pledged to work with UN envoy Kofi Annan to try to end the crisis.
In their statement, the leaders said that Syria's future must be worked out by "Syrians themselves" in the "framework of Syria's sovereignty, independence, unity, and territorial integrity."
Russia has been concerned to avoid a repeat of the international mission in Libya when it was assured the West was not bent on regime change, but then saw allied warplanes help the opposition topple dictator Moamer Kadhafi.
US officials have said they want Russia's help to create a political transition similar to that which ushered Yemen's president Ali Abdullah Saleh from power in February after a year-long uprising.
"From my point of view we have found many common points on this (Syria) issue," Putin said after the talks, adding that Russia and the United States will continue discussions on how to deal with the ongoing violence.
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It's uncertain how sincere Putin is to help solve the Syrian crisis, during which the world has been witnessing a new Cold War between the two old foes. Putin doesn't support Western-backed humanitarian efforts, believing they were aiming at topping a regime, which the West - especially the U.S. - deemed undemocratic.