Sitting in leather armchairs on opposite sides of a small table, the pair leaned forward in animated talks on the sidelines of a summit in Turkey's Mediterranean resort of Antalya, state television showed.
According to Russian news agencies, the pair met for 20 minutes.
The two heads of state held the summit in an unlikely venue, nearby a potted palm tree as other delegates wandered by and security agents partially obstructed the view of the television camera.
None of the content of the conversation was divulged to the journalists covering the summit.
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Hours earlier, the former Cold War foes shook hands as they took places for a family photograph of the Group of 20 top world economies, a summit now dominated by the Paris bombing and shooting assault, which killed 129 people.
It was Obama and Putin's first meeting since Russia launched its declared anti-Islamic State air bombardment in Syria at the end of September. The West suspects the campaign is really aimed at propping up Syrian President Bashar al-Assad.
But world leaders gathered in Turkey are seeking to put aside differences to deliver a united message against extremist attacks.
"We will only be able to deal with the terrorist threat... if all the international community unites its efforts," Putin said before his meeting with Obama.
Obama, moments after the Putin talks, arrived late to the main summit session just as fellow leaders were observing a moment of silence to remember the victims of terror in Paris and also Ankara last month where 102 people died.
Obama in 2013 had joked that Putin looked like "that bored schoolboy in the back of the classroom", adding to offence he caused in 2009 by saying the ex-KGB spy had "one foot in the old ways of doing business".