Nkoka broke clear of a three-man lead group, which also included countryman Warinyane Lebopo and South African debutant Hendrick Ramaala, in the latter stages of the race to win in 3:09:52.
The elite men’s field had targeted Thompson Magawana’s 26-year-old record of 3:03:44, with a R1 million bonus on the line, but after a fast start the pace gradually slowed.
“Some of the guys said they would try for the record, but they didn’t train properly for it and weren’t prepared,” Nkoka said.
“I was aiming to run under three hours and 10 minutes, so I’m very happy.”
While Ramaala dropped off the pace, allowing Lebopo to open a gap, he fought back to grab second place in 3:11:33 in his first ultra-marathon.
Masilo Matjiane of Lesotho also produced a late surge to finish third in 3:12:00, with Lebopo settling for fourth in 3:12:24 and long-time leader Ketema Tadesse of Ethiopia finishing fifth in 3:12:35.
“The people on the road really kept me going over the last few kilometres,” Ramaala said.
“At 42km I thought the race was over for me so I’m very grateful for their support.”
Podnebesnova, meanwhile, won the women’s race in 3:40:07, nearly 10 minutes outside Frith van der Merwe’s 25-year-old record.
The 34-year-old Russian had finished fifth in two previous attempts at the race.
“I prepared differently this year because I’ve changed to a new coach,” she said.
“I’m very happy to win and I’ll be back next year.”
Shitaye Gemechu Debellu of Ethiopia, who had made an early attempt at Van der Merwe’s mark and the lucrative financial incentive, finished second in 3:43:37.
Four-time winner Elena Nurgalieva of Russia, who said she had picked up flu in the build-up to the race, was third in 3:43:59.
Paulina Njeya was the first South African woman home, taking fifth position in 3:50:48.
National champion Stephen Mokoka won the men’s half-marathon in 1:04:16 and in-form Lebo Phalula secured victory in the women’s 21km race in 1:14:00.