The two men held closed door talks for 50 minutes at the Asia-Pacific Economic Cooperation summit in Peru on Sunday.
Both spoke in favour of free trade - including the Trans Pacific Partnership - defying the campaign rhetoric of US President-elect Donald Trump.
Prime Minister Malcolm Turnbull praised Mr Obama as a "remarkable leader".
"It's a momentous occasion when one president hands over to another," Mr Turnbull said.
"President Obama has been a remarkable leader of the United States and indeed leader of the world for eight years. There's an element of sadness there but a great sense of achievement too."
The two world leaders privately discussed security issues in the South China Sea and the fight against the Islamic State group.
Mr Turnbull also thanked the US president for his co-operation on the agreement to resettle asylum seekers held in offshore detention centres in Papua New Guinea and Nauru.
Mr Obama in return said it was "not often where I have a meeting and I've got nothing to disagree with".
"Usually there's something to keep us busy."
Mr Turnbull has pledged to work with Mr Trump, declaring on US election night that "Americans understand that they have no stronger ally, no better friend" than Australia.
He described his first conversation with Mr Trump as warm and constructive.
"I've Â­already had a good chat with the president-elect and I'm sure the very strong relationship between Australia and America will continue," he told local radio last week.
Australia's prime minister has taken a "farewell selfie" after his final meeting with Barack Obama as the US president.