The two met for 90 minutes, with Mr Putin emerging from the meeting saying it was "very useful and frank."
Their meeting came after world leaders had addressed a range of global topics in speeches to the annual UN General Assembly.
But much of the gathering has been dominated by the fighting in Syria.
The flood of Syrian refugees spilling beyond the neighbouring countries of the Middle East and now into Europe has brought a clear sense of urgency in talks at the United Nations.
With no immediate signs of success in bringing down the self-proclaimed Islamic State, or IS, the meetings in New York have focused on the best way forward in Syria.
Speaking at the UN General Assembly, United States president Barack Obama described Syria's President Bashar al-Assad as the chief culprit behind the four-year civil war.
At least 200,000 people have died in four-and-a-half years of fighting, and millions have been driven from their homes internally or abroad as refugees.
But Mr Obama has now voiced a willingness to work with Iran, which has armed the Syrian government, and Russia, recently engaged in a military build-up in Syria, its longtime ally.
"The United States is prepared to work with any nation, including Russia and Iran, to resolve the conflict. But we must recognise that there cannot be, after so much bloodshed, so much carnage, a return to the pre-war status quo."
The United States and Russia continue to clash over whether to work with Bashar al-Assad to stop I-S, also known as ISIL.
During their private meeting, Mr Obama told Mr Putin he believes there is no path to stability in Syria with Mr Assad in power.
Mr Obama also made it clear in his UN address.
"Yes, realism dictates that compromise will be required to end the fighting and ultimately stamp out ISIL. But realism also requires a managed transition away from Assad and to a new leader and an inclusive government that recognises there must be an end to this chaos so that the Syrian people can begin to rebuild."
But Vladimir Putin argues it is a huge mistake not to cooperate with President Assad.
"Russia has always been consistently fighting against terrorism in all its forms. Today, we provide military and technical assistance both to Iraq and Syria and many other countries of the region who are fighting terrorist groups. We think it is an enormous mistake to refuse to cooperate with the Syrian government and its armed forces, who are valiantly fighting terrorism face-to-face. We should finally acknowledge that no-one but President Assad's armed forces and Kurdish militia are truly fighting the Islamic State and other terrorist organisations in Syria."
In his meeting with Mr Obama, Mr Putin said it should be the Syrian people who decide the fate of Syria's president.
He also used his address to the UN General Assembly to call for a broad coalition to fight IS in Syria.
Mr Putin likened such a coalition to the so-called "anti-Hitler" alliance that fought together during World War Two, adding Muslim countries should play a key role.
He elaborated on that in his private meeting with Mr Obama, suggesting Iran, Saudi Arabia, Turkey and Jordan could join the future group.
Australia's Foreign Minister Julie Bishop has cautiously welcomed Russia's military involvement in Syria and the common goal she says Russia has with the United States.
But she says she hopes a level of cooperation can be reached between the parties to defeat IS, also known as Daesh.
"President Putin has said that the increase in military resources is in Syria for that purpose, for the purpose of assisting in the deterring and defeating of this brutal terrorist organisation, and we have to welcome that. But, of course, the coalition air strikes are designed to do precisely that, to disrupt, to defeat Daesh. Russia is working to that same end."
Finding a solution to the ensuing humanitarian crisis gripping Europe has also been a key talking point at the UN gathering.
France has announced it will discuss with its partners a proposal by Turkey and members of the Syrian opposition for a no-fly zone in northern Syria.
Refugees would then be allowed to live there under the plan.
In other key matters at the General Assembly, Mr Obama also used his speech to announce a boost to US peacekeeping forces and resources.
The new effort includes intelligence, helicopters, hospitals and troops.
And with France hosting climate-change talks late this year in Paris, President Francois Hollande announced a two-billion-euro increase in helping developing countries fight climate change.
The 70th UN General Assembly continues tomorrow.
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