Mr. Obama expressed his regret for the loss of a Russian pilot and crew member after Turkey shot down a Russian plane last week, according to a White House official.
The official also said that Mr. Obama told Putin again that Syrian President Bashar al-Assad must leave power as part of a political transition, a long-held U.S. position that remains at odds with Russia's support for Assad.
Putin spokesman Dmitry Peskov said the meeting lasted for 30 minutes. He said the two leaders discussed Syria in detail, and they both spoke in favor of moving toward the launch of a political settlement to Syria's civil war. Russia and the U.S. are both involved in a new diplomatic effort in Vienna to bring about a ceasefire, potentially within weeks.
Mr. Obama also called on Russia to focus its airstrikes in Syria on militants from the Islamic State in Iraq and Syria (ISIS), not rebels fighting Assad, the White House said.
The two leaders also discussed implementing a ceasefire in Ukraine.