On Tuesday Mr Obama cancelled planned talks after the firebrand Mr Duterte called him the "son of a whore".
Wednesday's informal meeting took place before an Asean summit gala dinner.
While a Philippine spokesman said he was "very happy" it happened, the US side said they had a "brief discussion" in a pre-meal "hold space" for leaders.
Mr Obama and Mr Duterte are said to have entered the dinner venue separately at the summit in Laos and did not interact with each other during the event, which lasted one hour and 20 minutes.
"They were the last people to leave the holding room. I can't say how long they met," Philippine Foreign Secretary Perfecto Yasay, travelling with Mr Duterte, told reporters shortly afterwards.
"I'm very happy that it happened."
A White House official said the pair exchanged "pleasantries" in a "brief discussion" before dinner.
War on drugs
Mr Duterte's outburst came after at a press conference where he told reporters he would not accept Mr Obama raising any concerns about the war on drugs in the Philippines.
"You must be respectful. Do not just throw away questions and statements. Son of a whore, I will curse you in that forum," Mr Duterte said, apparently in reference to the US president.
What else has the controversial Filipino president said?
Summit diplomacy, Duterte-style
World leaders' offensive insults: Who's top?
From 'Punisher' to president: Who is Rodrigo Duterte?
The  Filipino leader later expressed regret over the remarks, but not before Mr Obama had cancelled a planned meeting.
Mr Duterte won the presidency with his hard-line policy to eradicate drugs and some 2,400 people have died in anti-drug operations since he took office in June.
He had previously urged citizens to shoot to kill drug dealers who resisted arrest, and threatened to "separate" from the UN after it called his war on drugs a crime under international law.
President Duterte, known for his controversial remarks, had previously called US Secretary of State John Kerry "crazy" and referred to Pope Francis as the "son of a whore".
But the president also has staunch support at home for his hardline position on drugs.
US President Barack Obama and Philippine leader Rodrigo Duterte had a brief face-to-face encounter, days after a very public spat.