The two patients' virus levels became undetectable after bone-marrow therapy with stem cells.
They are still on antiretroviral therapy (ART) "as a precaution", but those drugs alone could not be responsible for bringing the virus to such low levels, said David Cooper, director of the Kirby Institute at the University of New South Wales in Sydney, who led the discovery.
Cooper began searching for patients who had been purged of the HIV virus after attending a presentation by a US team last year at a conference of the International AIDS Society in Kuala Lumpur.
At that meeting, researchers from Brigham and Women's Hospital in Boston, Massachusetts, reported that two patients who had received stem-cell transplants were virus-free.
Cooper and his collaborators scanned the archives of St Vincent's hospital in Sydney, one of the largest bone-marrow centres in Australia.
"We went back and looked whether we had transplanted [on] any HIV-positive patients, and found these two," said Cooper.
The first patient had received a bone-marrow transplant for non-Hodgkin's lymphoma in 2011.
His replacement stem cells came from a donor who carried one copy of a gene thought to afford protection against the virus. The other had been treated for leukaemia in 2012.
Because of the risk of relapse, Cooper's team will not claim that their patients are cured, 'nature.com' reported.
However, Cooper said the results show that "there is something about bone-marrow transplantation in people with HIV that has an anti-HIV reservoir effect, such that the reservoirs go down to very low levels. And if we can understand what that is and how that happens, it will really accelerate the field of cure search."
Stem-cell transplant in itself cannot be used as a routine HIV treatment, because of the high mortality (10 per cent) associated with the procedure, researchers said.
Earlier this month, the search for AIDS cure suffered a major setback when a child in the US, who was thought to have been cured of HIV after intensive drug therapy, was found with detectable levels of the virus.