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Fighting back in the latter stages of the 42.2km race, Tjoka crossed the finishing line in 2:43.40 to break Rene Kalmer’s two-year-old mark by 14 seconds.
South African Michael Mazibuko held off the Lesotho charge to win the men’s title in 2:19.04.
The leaders of the men’s race went to halfway in record pace, crossing the 21km mark in 1:07.31 ahead of a large chasing pack including last year’s top four finishers.
Sityhilo Diko made the first real break shortly after halfway, but he was swallowed up by the chasing group of nine as they stormed ahead with 8km to go.
Mazibuko, having done all the hard work after the pack hit the front, tore clear up Heartbreak Hill with less than 4km remaining.
He admitted he had been intimidated by a chasing group that trained together in the mountains of Lesotho, and had dominated SA road races in recent years.
“I was worried about the guys from Lesotho, but I told myself they are people, just like me, and I would not let them beat me,” he said.
Moeketsi Mosuhli pushed hard to narrow the gap in the closing stages, but settled for second in 2:19.05.
Defending champion Lebenya Nkoka took third place in 2:19.34, with five men from Lesotho finishing among the first seven.
Tjoka, meanwhile, looked to be in trouble in the second half as she clutched her chest and shortened her stride.
Having strung out the women’s field, she was caught and passed by Zimbabwean Sharon Tavengwa with less than 10km remaining.
Fighting back, Tjoka found her second wind, and held off a late charge from Emma Gooderham of Great Britain.
Tjoka said she had been a little concerned after Tavengwa went past, but had made an effort not to panic.
“I pushed harder to get past her again,” Tjoka said.
“I knew I had done the training and I stayed focused.”
Gooderham, 40, recovered from an early fall to finish second, with a nasty bruise on her shoulder, in 2:43.57.