A study in Nature magazine suggests the species may have lived in Gorham's Cave on Gibraltar up to 24,000 years ago.
The Neanderthal people were believed to have died out about 35,000 years ago, at a time when modern humans were advancing across the continent.
The new evidence suggests they held on in Europe's deep south long after the arrival of Homo sapiens.
The research team believes the Gibraltar Neanderthals may even have been the very last of their kind.
"It shows conclusively that Gorham's Cave today was the last place on the planet where we know Neanderthals lived," said lead author Professor Clive Finlayson, director of heritage at the Gibraltar Museum.
Tool technology
Though once thought to have been our ancestors, the Neanderthals are now considered an evolutionary dead end.
They appear in the fossil record around 230,000 years ago and, at their peak, these squat, physically powerful hunters dominated a wide range, spanning Britain and Iberia in the west to Israel in the south and Uzbekistan in the east.
Our own species, Homo sapiens, evolved in Africa, and displaced the Neanderthals after entering Europe about 40,000 years ago.
The cave has given up a range of Neanderthal artefacts (Image: Gibraltar Museum)
Researchers from Britain, Gibraltar, Spain and Japan obtained radiocarbon dates on charcoal from ancient hearths unearthed deep inside Gorham's Cave on Gibraltar, a mountainous peninsula on the southern tip of Iberia.
The charcoal comes from ground layers in the cave where archaeologists previously dug up stone tools of a type, or style, known as Mousterian, which, in Europe, is associated with Neanderthals (Homo neanderthalensis).
The earliest samples of charcoal date to 33,000 years ago, while the youngest date to 24,000 years ago - much more recent than anyone could have imagined.
But evidence for a presence 24,000 years ago is limited, so the researchers can only say with confidence that Neanderthals were in the cave until 28,000 years ago.
Rich resources
Even so, this date makes the cave the youngest Neanderthal occupation site known anywhere.
Scientists believe it was a favoured spot where hunting groups sought refuge from cold weather during the last Ice Age.
The rock shelter is well ventilated and relatively well illuminated; a high, vaulted roof meant smoke from the Neanderthals' fires would have risen away from the cave floor, instead of lingering at ground level and choking the occupants.
How Gibraltar might have looked in Neanderthal times
More details
And because sea levels were lower at this time, Gibraltar was surrounded by a coastal plain, rather than water. Covered by marshes in some places and in others by sand dunes, the plains were a habitat for a rich array of animals.
Professor Chris Stringer, from London's Natural History Museum, said the rock would have made for a good vantage point for Neanderthal hunters: "Excellent if you're trying to map your resources and decide where your next meal is coming from," he said.
"On top of the rock, there might have been things like ibex; out on the plains there would be deer, possibly horses and rabbits. We know they were eating shellfish and even tortoises - the poor things were probably being baked in their shells."
Dramatic switch
Commenting on the work, Katerina Harvati, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, pointed out that the new dates were "from charcoal found in Mousterian levels, not from Neanderthal bones. No Neanderthal fossils have been found in those layers."
"It is assumed that the Mousterian stone tools were made by Neanderthals... this is a reasonable assumption, though still an assumption."
But, she added: "The dates reported by Finlayson and colleagues are the first definitive, well-documented evidence for the survival of Neanderthals past 30,000 years ago."
Chris Stringer thinks the site provides an important insight into the reasons for Neanderthal extinction.
"For years, many of us have tended to look for one single reason why Neanderthals died out - that we interbred with them, or out-competed them, or killed them off. The Gibraltar evidence fits into a picture that has been emerging in recent years of quite a complex event," he explained.
"The idea of modern humans coming in and Neanderthals dying out simply didn't happen."
One view of Neanderthal extinction has them rapidly vanishing as modern humans swept across Europe. Modern man is a suspect, but the new evidence supports an important role for climate change.
In the end, rapid climate change may have doomed the species
The Neanderthals survived in local pockets during previous Ice Ages, bouncing back when conditions improved. But the last one appears to have been characterised by several rapid and severe changes in climate which hit a peak 30,000 years ago.
These were probably more dramatic in more northerly parts of Europe, where they may have upset the balance between Neanderthals and modern humans, allowing moderns to gain the upper hand.
Gibraltar's climate was sheltered from many of these changes, but it did eventually deteriorate. Recent deep-sea core data show that temperatures dropped sharply around 24,000 years ago. This could have created drought-like conditions in the area which may also have reduced the number of prey the Neanderthals could catch.
"If you've got a shrinking Neanderthal population on the edge, it might just be enough to tip them over the edge," Professor Finlayson told BBC News.
Co-author Jose Carrion, from the University of Murcia, Spain, suggested excessive inbreeding could also have been a factor in their demise.
Details of the work will be presented here at the Calpe conference, which runs from 14-17 September in Gibraltar.
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