Named Homo naledi, the species has been assigned to the genus Homo, to which modern humans also belong.
Scientists unearthed more than 1,500 bones belonging to at least 15 individuals which are yet to be dated
They say they could be anything between 20,000 and two million years old.
The discovery came about thanks to a tip-off from cavers two years ago, who had glimpsed what looked like human remains through a crack in a limestone wall.
The bones were located in the Rising Star cave system in South Africa's Gauteng province, part of the Cradle of Humankind World Heritage Site, in a remote chamber that can only be accessed via several steep climbs and fissures.
The chamber, situated down a narrow 40ft (12 metre) chute, measures around 30 feet (9 metres) long and just a few feet wide, National Geographic reported.
It is not yet clear how more than a dozen H. naledi skeletons - ranging from babies to elderly individuals - ended up in a remote region of a large cave.
The researchers have not ruled out the possibility of the bodies being disposed of in the cave deliberately, or a catastrophic 'death trap' scenario in which the humans entered the cave and all died of an unknown cause.
If the burial scenario is correct, the creatures would have introduced artificial light into the caves in the form of torches as the narrow passages are entirely devoid of light.
The bones are in phenomenal condition - with even the delicate inner ear bones of the new species lying intact.
Professor Chris Stringer, Research Leader in Human Origins at the Natural History Museum in London, said: 'The deep cave location where the bones were found suggests that they may have been deposited there by other humans, indicating surprisingly complex behaviour for a 'primitive' human species.'
Scientists say that many more examples of the new species may lay uncovered in the remote cave system.
The finding has provided a challenge for the international team of scientists who have been tasked with analysing and aging the bones, Dr Stronger added: 'Some of Homo naledi's features, such as its hands, wrist and feet, are very similar to those of modern humans.
'On the other hand, the species' small brain and the shape of its upper body are more similar to a prehuman group called australopithecines.'
'While we do not yet know the exact age of the bones, the discovery of so many fossils belonging to at least 15 individuals is remarkable.
'The mixture of features in H. naledi highlights once again the complexity of the human family tree and the need for further research to understand the history and ultimate origins of our species.'
It is hoped Homo naledi will shed light on the transition from australopithecines to humans, helping uncover how humans fit into the framework of the natural world over the course of their evolution.
Australopithecines emerged around four million years ago and had a brain no larger than a chimp's.
The species is epitomised by 'Lucy', a skeleton discovered in Ethiopia in 1974. About a million years passed before Homo erectus, or modern man, began to emerge and much of how human evolution played out over this time remains shrouded in mystery.
Scientists admit that it could take decades before they are able to identify who Homo naledi really was and how he fits into our complex evolutionary tree.
Professor Stringer added: 'The mixture of features in H. naledi highlights once again the complexity of the human family tree and the need for further research to understand the history and ultimate origins of our species.'
Casts of Homo naledi fossils will be unveiled at the Natural History's after-hours Science Uncovered event on 25 September and will then go on permanent display in a new Human Evolution gallery opening at the Museum at the end of November.
At the event, they will be alongside the reconstructed skeleton of a recently discovered australopithecine species from South Africa: Australopithecus sediba.
Comparing the characteristics of these ancient species reveals how humans have changed over millions of years.
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