The man who had been living in a wheelchair for two decades has lost most of his body in a rare cancer-related death.
He was 62.
The condition was terminal and he died last week, the South African Medical Research Council said in a statement on Friday.
It was not clear why the man died.
The man was the first patient to have died from cancer of the blood and organs.
The SRC has confirmed he was a patient who had tested positive for the cancer.
The World Health Organization (WHO) has called the cancer a major global public health emergency.
A statement from the WHO said the man’s death was the result of “unprecedented” and “unusual” medical care.
It said it was working closely with the WHO to find out the cause of the death.
The WHO says cancer is the leading cause of death worldwide.
The BBC has not been able to reach the man for comment.
WHO Director-General Margaret Chan said it is “not uncommon for cancer patients to undergo surgical procedures, but it is unusual for someone to die of cancer”.
The WHO said a special committee will be established to investigate the death and “assess the reasons and mechanisms behind it”.
WHO Director General Margaret Chan speaks to journalists in Geneva.
The statement said WHO has been providing “all relevant information to the investigating committee”.
It said the case raises a number of questions about the way the health system is managed, including how much it should be paying for the care of patients with cancer, and whether it is appropriate for patients to be treated at home, or for patients who have undergone surgery, in a ward.
WHO has launched an investigation into the death of the man, who had a previous heart attack.
WHO’s director-general, Margaret Chan, has called on the world’s health organisations to work together to help patients living with cancer.
WHO, the World Health Organisation, the UN agency for refugees, the International Monetary Fund, and several other governments have said the world is on the brink of a pandemic.