“The two parties have confirmed their desire to intensify coordination between the Russian and American militaries in Syria,” the Kremlin said in a statement.
Putin also called on Obama to help aid the separation of moderate opposition groups from “terrorist groups like the Al-Nusra front”, it said.
They both stressed the importance of restarting UN-sponsored Syria peace talks after two rounds of negotiations held in Geneva since the start of the year ended without progress.
During a visit to Georgia ahead of a NATO summit, US Secretary of State John Kerry welcomed Wednesday the 72-hour ceasefire announced by the Syrian army to coincide with Eid al-Fitr which marks the end of the holy fasting month of Ramadan.
He added that he hoped a more long-term cessation of hostilities will follow.
The last truce in the country was declared on February 27 between regime and non-jihadist rebel groups after being brokered by Russia and the US.
Though it did not apply to the battle against jihadist factions, it sharply reduced violence in the conflict that has so far claimed more than 280,000 lives and displaced millions of people.
The ceasefire all but collapsed after repeated violations.