The two men met ahead of the Group of 20 summit as Obama sought to ease tensions between the two, the White House said. It was their first meeting since Putin returned to the presidency six weeks ago.
The meeting was followed by a session between Obama and German Chancellor Angela Merkel.
Despite their differences, Putin said he and Obama were able to find many commonalities on issues, including Syria. Obama said the meeting was a "candid, thoughtful and thorough conversation" on range of issues.
"We agreed that we need to see a cessation of the violence, that a political process has to be created to prevent civil war," Obama said.
"We are united in the belief that the Syrian people should have the opportunity to independently and democratically choose their own future," Obama and Putin said in a joint statement.
The two leaders reaffirmed their commitment to strengthening close and cooperative relations.
"In recent years, we have laid a solid foundation for expanding our bilateral interaction in a variety of areas," the joint statement said. "Today we agree to continue this work guided by the principles of the rule of law, respect for human rights, equality, and mutual respect."
Obama and Putin also discussed Iran and agreed there's still "time and space" for diplomacy, he said.
On the issue of missile defense, however, Obama said there is still the need to work through difficult problems.
"President Putin clearly is somebody who can articulate where he has differences with the United States, but we can also articulate where we have differences with Russia," deputy national security adviser Ben Rhodes said at a White House press briefing prior to the meeting.