The remarkable discovery suggests Aboriginal people lived in the Adnyamathanha region, 550 kilometres north of Adelaide, 49,000 years ago - 10,000 years earlier than previously thought.
After nine years of research, it was a chance discovery that unearthed the rich prehistoric site.
"We kind of just came across it," traditional owner of the Flinders Ranges Clifford Coulthard told NITV.
"We went for a toilet stop and found a spring and some engravings and we followed that valley down and found this shelter."
Mr Coulthard says the Warratyi (emu) rock shelter has special significance to the Adnyamathanha people.
"It's so peaceful, very spiritual land. It was good to work in that shelter, a good feeling."
Assisted by members of Adnyamathanha Traditional Lands Association, a team of archaeologists sifted through 3.3 tons of dirt, recovering 4300 artefacts and 200 fragments of bone.
"It's got ochre in it, it's got emu eggshell, it's got plant material, about three kilos of bone...and that's all dating back to about 49,000 years," Principal Researcher Giles Hamm told NITV.
The discovery makes the arid region of South Australia one of the earliest sites of human occupation in the country.
"Talk about gobsmacked, I was totally shocked," Mr Hamm recalled.
"To find these dates getting older, and older, and older it was just extraordinary."
Among the objects uncovered was a hand-made sharpened bone point. It's the oldest bone-tool ever found in Australia and pushes back previous earliest-known dates on the development of bone and stone axe technologies.
"That point has been used to pierce the skins of animals, so particularly animals like kangaroo and wallaby, so that's a sort of needle-like tool," Mr Hamm explained.
The shelter also contains the first evidence of human interaction with long-extinct megafauna.
Professor Gavin Prideaux from the school of Biological Sciences at Flinders University says bones from a giant wombat-like animal called Diprotodon optatum and eggs from a large emu-like creature were two significant discoveries.
"Considering the nature of the deposit itself, where that rock shelter is, there's no way that an animal like a Diprotodon could have scaled up that steep slope, and got into that rock shelter, any other way than to be brought there, dead, by people."
Professor Prideaux told NITV evidence that Aboriginal ancestors and megafauna lived at the same time, in the same place, raises questions about whether humans played a role in their extinction.
"These findings in and of themselves do not demonstrate that humans drove the megafauna extinction.
"But what it does do, that's significant for the megafauna debate, is that it demonstrates that people exploited these animals, they actually used them for food and lived at the same time."
Aboriginal elder Clifford Coulthard from the Adnyamathanha Traditional Lands Association told NITV he fears plans to dump waste in South Australia will harm the region's rich historical sites.
"If the waste dump gets too close to shelters, like Emu, it could have an effect because there's more work to be done there that could even go back another couple thousand years."
Researcher Giles Hamm hopes the discovery will lead to further exploration of Aboriginal history in outback Australia.
He plans to return to the shelter and continue his work digging up Indigenous Australia's history.
"It's a really exciting time for uncovering a very, very rich and sophisticated Aboriginal history in this part of Australia."
The full report outlining the historic findings has been published in Nature.