The surprising discovery came after researchers analysed unusually well-preserved DNA from the fossil.
Their findings, reported in the journal Nature, confirmed the specimen came from a young girl who was neither "modern human" nor Neanderthal.
Instead she belonged to a separate, now extinct, branch of the human family tree which scientists have named Denisovians, after the Denisova Cave in southern Siberia where the fossil was found.
A molar tooth recovered from the cave is also believed to be from a Denisovian individual.
It looks different from the teeth of modern humans and Neanderthals, and more closely resembles those of older human ancestors such as Homo erectus.
The finds alter the story of human evolution, suggesting the Neanderthals had an Asian sister group that broke away on its own evolutionary path before dying out.
Most scientists believe ancestors of the Neanderthals left Africa between 300,000 and 400,000 years ago to establish themselves in Europe and Eurasia. Meanwhile, the direct ancestors of modern humans, Homo sapiens, remained and evolved in Africa.
They headed out of Africa 70,000-80,000 years ago and for a time co-existed with the soon-to-be-extinct Neanderthals.
Now scientists believe the Denisovians diverged from the Neanderthals at the time of the original exodus and spread east.
Like the Neanderthals, they appear to have interbred with modern humans.
The evidence came unexpectedly when Denisovian gene sequences turned up in the DNA of modern Melanesian Pacific islanders. The research suggests genetic material derived from Denisovians makes up around 4-6 per cent of the genetic code of at least some Melanesians.
Richard Green was one of the scientists from the University of California at Santa Cruz, who took part in the DNA analysis.
He said: "Instead of the clean story we used to have of modern humans migrating out of Africa and replacing Neanderthals, we now see these very intertwined storylines with more players and more interactions.
"This study fills in some of the details
"But we would like to know much more about the Denisovians and their interactions with human populations."
Mr Green added: "You have to wonder if there were other populations that remain to be discovered. "