"We can confirm that these two rhinos (a male and a female) were not poached," the South African environment department and Chad government said in a joint statement. "However, the exact cause of death is not yet known."
In July, there was widespread outrage and a bitter row over responsibility when 11 black rhinos in Kenya died after being transferred to a new sanctuary, mainly due to toxic levels of salt in borehole drinking water.
The rhinos in Chad had been roaming free in Zakouma National Park since late August after a gradual acclimatisation process that saw them first released into small enclosures.
The carcasses of the cow and bull were discovered on October 15.
The surviving four rhinos are being closely monitored, the statement said, adding that a specialist veterinarian had travelled to the park to conduct postmortems.
It said the cause of death would be announced as soon as possible.
Project hailed as 'truly hopeful'
In May, the six rhinos were sedated with darts, put in special ventilated steel crates and driven under police escort from Addo park in South Africa to Port Elizabeth airport.
They were then flown to Chad on a 3,000-mile (4,800-kilometre) flight, accompanied by a team of vets checking their stress levels.
The high-profile transfer, which took two years of planning, was hailed as major conservation breakthrough, with translocation organiser African Parks describing it as a "truly hopeful story".
There are fewer than 25,000 rhinos left in the wild in Africa due to a surge in poaching, and only 5,000 of them are black rhinos.
Black rhinos are rated as critically endangered by the International Union for Conservation of Nature.
Rhinos are targeted to feed a booming demand for rhino horn in China, Vietnam and other Asian countries, where it is believed to have medicinal qualities.
jpegMpeg4-1280x720Northern white rhinos disappeared from Chad several decades ago and the last western black rhino was recorded there in 1972, after decades of poaching pushed both subspecies to local extinction.
Rhinos were re-introduced to Rwanda in 2017.