The survey, by the government-funded Medical Research Council and non-profit organisation Gender Links, found that 37.4 per cent of men in the north-central province of Gauteng admitted to committing rape at some point in their lives, while 25.3 per cent of women said they had been victims of rape.
It follows up on a national survey carried out last year that found that more than one in four South African men admitted to having raped a woman or girl.
"The previous level was so high that we didn't expect it to be even higher," Rachel Jewkes, a researcher at the Medical Research Council, told AFP.
Researchers surveyed 487 men and 511 women in Gauteng, the country's second-most populous province, which is home to Pretoria, the capital, and Johannesburg, the largest city.
The study group was 90 per cent black and 10 per cent white, reflecting the province's demographics, authors said.
Over half the women surveyed said they had experienced some form of violence -- emotional, economic, physical or sexual -- in their lifetimes, and 78.3 per cent of men admitted to perpetrating some form of violence against women.
South Africa has one of the world's highest rates of reported rape, with 36,190 cases -- 99 per day -- reported to police in 2007, but experts say that only a small number of attacks are actually reported.
The MRC study found that only one in 25 rapes had been reported to the police.
South Africa has the highest number of HIV infections in the world, compounding the trauma rape victims face.
In the 2009 study, one in five confessed rapists tested positive for HIV.
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