Researchers at the Harvard School of Public Health (HSPH) said the policies of Thabo Mbeki, who was heavily criticized during his 1999-2008 presidency for the denial of scientific remedies for AIDS, contributed directly to the deaths.
"Many lives were lost because of a failure to accept the use of available (antiretroviral drugs) to prevent and treat HIV/AIDS in a timely manner," researchers said.
Mbeki's health minister, Manto Tshabalala-Msimang, was widely discredited for proposing lemon juice, olive oil, garlic and beetroot as AIDS treatments as the country battled one of the world's worst AIDS epidemics.
Some 5.5 million of the 47 million population are infected by HIV -- over 18 percent of the adult population.
The study, published online last month and available Monday in the Journal of Acquired Immune Deficiency Syndromes, said the country lost at least 3.8 million years of life from the 330,000 adults who died for lack of proper treatment and the 35,000 babies who died after they were born with HIV.
For the study's model researchers compared the policies of the South African government with those of neighbouring Botswana and Namibia, which are suffering from comparable epidemics and did enforce a policy of treating patients with appropriate drugs.
According to the World Health Organization, 33 million people around the world are infected with the AIDS virus, mostly in the sub-Sahara Africa.
Some two million people died worldwide of AIDS in 2007.