The Deep Skull was also likely to have been an older woman, rather than a teenage boy, researchers said.
The study represents the most detailed investigation of the ancient cranium specimen since it was found in Niah Cave in Sarawak, Malaysia in 1958.
"Our analysis overturns long-held views about the early history of this region," said Darren Curnoe from University of New South Wales in Australia.
The Deep Skull was discovered by Tom Harrisson of the Sarawak Museum during excavations at the West Mouth of the great Niah Cave complex and was analysed by British anthropologist Don Brothwell.
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In 1960, Brothwell concluded the Deep Skull belonged to an adolescent male and represented a population of early modern humans closely related, or even ancestral, to Indigenous Australians, particularly Tasmanians.
"Brothwell's ideas have been highly influential and stood largely untested, so we wanted to see whether they might be correct after almost six decades," said Curnoe.
"Our discovery that the remains might well be the ancestors of Indigenous Bornean people is a game changer for the prehistory of South-East Asia," added Ipoi Datan from Sarawak Museum.
The Deep Skull has also been a key fossil in the development of the so-called "two-layer" hypothesis in which South-East Asia is thought to have been initially settled by people related to Indigenous Australians and New Guineans, who were then replaced by farmers from southern China a few thousand years ago, researchers said.
It also suggests that at least some of the Indigenous people of Borneo were not replaced by migrating farmers, but instead adopted the new farming culture when it arrived around 3,000 years ago, researchers said.
The findings were published in the journal Frontiers in Ecology and Evolution.