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.
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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.

It happened at about 20:30 GMT on Saturday at the Antrim Road shop.
Two men wearing hooded tops made a purchase, then one asked the assistant for another item. When she opened the till, one of the men brought out a knife.
He lunged towards the woman, jabbing the knife in her direction. The second man them removed cash from the till.
Both were challenged by a male member of staff as they left and one of the robbers took the knife out again. They then fled on foot.
Neither member of staff was injured, but police said they were left very badly shaken.
Detectives have appealed for witnesses to contact them.

Chartoff's daughters confirmed he died at home in Santa Monica surrounded by his family. He had pancreatic cancer.
"He was an amazing father and person," said Julie Chartoff, adding: "There are no words."
He won the best picture Oscar for the first Rocky film in 1977, which was written by its star Sylvester Stallone.
The producer shared the Academy Award - one of three for the 1976 film - with partner Irwin Winkler.
They both went on to produce all seven Rocky movies, including the forthcoming film Creed, which is currently in post-production.
Chartoff was also nominated for an Oscar in 1981 for Raging Bull, Martin Scorsese's darker take on the sport, which starred Robert De Niro as boxer Jake La Motta.
He produced films into his late 70s and early 80s, including 2014's The Gambler with Mark Wahlberg and 2013's Enders Game with Harrison Ford.
He also worked on Jane Fonda's They Shoot Horses, Don't They? and 1983 film The Right Stuff, which won four Oscars.
Chartoff and Winkler - who worked together until 1985 - convinced United Artists to make Rocky for less than $1 million (Â£646,000), after Stallone insisted on playing the lead, according to Variety.
The film went on to earn 10 Oscar nominations and take more than $200m (Â£129m).
Chartoff is survived by third wife Jenny Weyman and his five children.
US President Barack Obama and Philippine leader Rodrigo Duterte had a brief face-to-face encounter, days after a very public spat.
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A woman working in an off-licence has been threatened with a knife during a robbery in north Belfast.
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Oscar-winning producer Robert Chartoff, who was behind hit boxing films such as the Rocky series and Raging Bull, has died in California, aged 81.