Last year, only 70 people died from the mosquito-borne disease, compared to 460 deaths recorded in the year 2000, said the report delivered at a Pan African Malaria conference in Durban.
The number of people who caught malaria has come down to about a 10th of the cases recorded that same year.
"South Africa is well on its way to being a malaria-free country," Health Minister Aaron Motsoaledi said.
Worldwide the disease kills an estimated 660,000 people each year, 90 percent of them in Africa with the majority being children.
Countries severely affected by malaria in the continent include Nigeria, the Democratic Republic of Congo, Tanzania and Mozambique.
Authorities in South Africa believe the continent's wealthiest and most developed country is closer to eradicating malaria, but admit that there was no quick fix.
They aim to rid the country of the disease by the year 2018.
At the centre of the fight to eliminate infections is the use of the highly contentious insecticide dichlorodiphenyltrichloroethane, better known by its acronym DDT, to kill the malaria transmitting vectors.
The chemical, which is sprayed inside houses, is linked to genital birth defects, infertility and cancer and is banned in many parts of the world.
After being halted in 1996, South Africa reintroduced it in 2000 as part of a plan to curb a major malaria outbreak.
Authorities say infections soared to more than threefold in 1996 after DDT was halted, rising to 64,500 in 2000.
"This was rapidly halted by combining DDT and pyrethroids for malaria vector control in the three malaria-endemic provinces."
According to the report, the insecticide has been used cautiously in recent years, "with targeted spraying only in high risk areas".
Its safety has always been questioned, with local authorities maintaining that it is less expensive but more effective amid a spike in insecticide resistant vectors in recent years.
Those at the receiving end of DDT are normally impoverished households in the northeastern Limpopo region, which borders Mozambique and the part of the southeastern province of KwaZulu Natal, where malaria is endemic.
Prevention has seen cases drop to less than one per 1,000 people in affected districts, according to the report.
The report stated that some households refused to have their houses sprayed, saying the chemical left stains on walls --signalling the lack of knowledge about health effects.
"Strategies need to be well thought out, practical, systematically and robustly implemented," said Motsoaledi.
University of Pretoria's professor Tiaan de Jager acknowledged the adverse genetic and hormonal risks linked with DDT, adding however that its efficacy cannot be discounted.
"We are not saying that people should rather die than using DDT," he said.
A combination of factors like improved housing and sanitation and education around the disease should form part of the control strategies.
"We can't rely on DDT, we should also look at safer methods that can lead to elimination," said De Jager.
This week researchers at the Durban conference revealed that a groundbreaking vaccine could be available by 2015.
GlaxoSmithKline is seeking approval for the prototype vaccine that reduces the risk of malaria by almost half among children aged between five and 17 months.
If it gets the green light, the vaccine is likely to be distributed through agencies such as UNICEF and the GAVI Alliance, a public-private health partnership.