At the time they had no idea how significant the find was, Mr Hamm admitted, and thought maybe it would reach back about 5,000 years.
Working with the Adnyamathanha people over the past nine years, Mr Hamm and colleagues recovered from the one-meter-deep excavations around 4,300 artifacts and 200 bone fragments from 16 mammals and one reptile.
Importantly dating of the artifacts and fossil finds show humans occupied the site from 49,000 to 46,000 years ago.
Mr Hamm said the significance of the site was the combination of its age and geographic location.
The previous oldest-known site in the arid zone, located at Puritjarra in western Central Australia, is around 38,000 years old.
However, Mr Hamm said it was likely the climate was more favorable when they arrived.
"They got there before it became really arid," he said.
"In one sense they were trapped in the Flinders Ranges because once the climate changed [due to the last glacial maximum] it was too risky to move out of these well-watered ranges that had these permanent springs."
It was a view supported by palaeoanthropologist Michael Westaway at Griffith University, who was part of a recent genomic study that confirmed modern Aboriginal Australians are the descendants of the first people to inhabit Australia and showed they adapted genetically to survive in the desert.
"Our DNA paper suggested the arid center at 50,000 years ago was not really a barrier to the movement of people, and this seems to be what Giles is suggesting - people were able to migrate south quite quickly," Dr Westaway said.
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Among the other significant artifact finds at the site was the earliest-known use of ochre in Australia and South-East Asia around 49,000-46,000 years ago.
Mr Hamm said they had pushed back the dates on the development of technologies such as bone needles (40,000-38,000 years ago), wood-handled stone tools (at least 24,000 years ago) and gypsum use (40,000-33,000 years ago).
The site also provided reliably dated evidence of hafted axe technology about 38,000 years ago.
Co-author Professor Gavin Prideaux pointed to the discovery of bones from the extinct giant wombat-like Diprotodon optatum and eggs from an ancient giant bird as important evidence of interaction with ancient humans which would have an impact on the debate over the extinction of megafauna.
Professor Prideaux, from Flinders University's School of Biological Sciences, said the only previous site in Australia where megafauna remains and human artifacts had been found together was Cuddie Springs in NSW, which had become the subject of controversy over the accuracy of dating.
"One good thing about this study ... is there's no doubt there are megafauna remains in the form of Diprotodon and a giant bird in that rock shelter in a well-dated, well-stratified context sometime between 45,000 and 50,000 years ago," Professor Prideaux said.
"The only way those bones and shells got there [because of the steep incline up to the rock shelter] is because people brought them there [to eat] ... in terms of megafauna that's the really significant finding."
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Professor Prideaux said the discovery was an important milestone in the debate over whether humans or climate change drove the extinction of megafauna.
"[The find] undermines one of the supposed pillars of support for climate change, not humans, causing the extinctions because [the Warrayti site shows] humans lived alongside these animals and hunted them," he said.
Professor Prideaux said the paper, published yesterday in Nature, "smashed several paradigms about Indigenous Australians".
Dr Westaway supported this view.
"There is a Eurocentric view that material culture in Australia is quite simplistic and backward, but this helps rewrite that story," he said.
Mr Coulthard, of the Adnyamathanha Traditional Lands Association, said he had worked on the property where Warratyi was located when he was a teenager.
The elders he had worked with had told him their people had lived in the area and had pointed out a lot of the shelters.
He had forgotten the information until he teamed up with Mr Hamm and believed "the spirits showed me the road" to the site.
He said the Adnyamathanha people were proud and happy about the discovery and interested to know how it would be received.