A ceremony was held as the remains were handed over to representatives of the Australian government’s Indigenous Repatriation Programme.
The skeleton was bought for £15 from a London trader over 100 years ago. Now, the man will be laid to rest in his homeland, as close as possible to the spot where he was originally buried.
It is unclear how the remains were used in Lund, but the university's Vice-Chancellor said he believed they may have been used in anatomy lessons.
“What I feel most strongly about is how he came here to begin with, how my earlier colleagues looked at this almost like animal remains. There was certainly some racial biology behind it, so these are not positive thoughts,” Vice-Chancellor Torbjörn von Schantz told TT.
“I feel a strong happiness and pride to be part of this process, to return these remains to their homeland and roots and in some way ensuring that they have their dignity restored,” he added.
Australia's ambassador Jonathan Kenna said the return “means a lot for all Australians” and helped to promote “healing and reconciliation”.
In total, almost 1,500 human remains of Aboriginal and other indigenous people have been returned to Australia, including from the UK, USA, Germany and the Netherlands, as part of the Indigenous Repatriation Programme.
Lund previously returned the remains of two other Aboriginal people to Australia in 2008, but at that time the skeleton which was handed over on Wednesday was missing. It was found in 2013 in a museum-run medical history collection.
In 2011, Lund University returned the remains of three Maoris to New Zealand, and in 2005 the university handed over the remains of a Russian Jewish man to the Jewish congregation in Malmö.