Twenty minutes before Bolt won his third successive 100 metres title, the South African ran at an unrelenting pace to clinch the gold medal and break Michael Johnson's 17-year-old 400 metres record in a time of 43.03 seconds.
It was the oldest standing men's sprint record - Bolt owns the 100 and 200 metres marks, - and one many thought might never be broken.
"I believed it was possible," the 24-year-old said. "I am just glad things went my way tonight.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
"I'm still a bit amazed, I still have to pinch myself with what just happened."
Van Niekerk's achievement was all the more remarkable for the fact that he ran in lane eight, the outside lane where it is impossible to see any of your rivals.
"I don't think any athlete wants to be in lane eight but I figured it (has) advantages as well as disadvantages," he said.
"You have the perfect opportunity to go out as if you are in training and go as hard as you can."
Van Niekerk has been training with Bolt's team this year and the Jamaican, who has said he will retire after the world championships in London next year, ran over to congratulate him after finishing the 100 metres.
"When he got the world record I was like, wow!" Bolt, who gave up the 400 metres because he did not like the training, told reporters.
"I told him in Jamaica 'my coach said you're probably the only guy right now other than me who can break this 400m world record'.
"I'm really happy for him, I'm really proud of him."
Van Niekerk, who also won the world title last year, said he was just happy to be at his first Olympics alongside the likes of Bolt, who he described as the "king of the sprints".
"I'm just really grateful that I'm part of this generation of athletics, just keeping the sport alive," he said.
"I use these guys as inspiration and motivation but I've now got a chance to build my own legacy, my own journey and story, hopefully I can inspire other South Africans and athletes around the world to go out and do their thing."
Van Niekerk watched the last Olympics at home on television but had a straightforward message for anyone who suggested his remarkable progress in the last four years was down to doping.
"I know I'm not, so what else can I say on that?" he said.
Twice Olympic 400 metres champion Johnson was dumbfounded by the quality of Van Niekerk's run.
"Van Niekerk is so young, what else can he do? Can he go under 43 seconds? It is something I thought I could do, but never did," the American said. "Usain Bolt will be retiring soon, this could be the next star."
When asked how fast he could run, Van Niekerk's reply would have been music to the ears of the International Association of Athletics Federation (IAAF), who have been unable to shift the cloud of a doping scandal that has overshadowed the sport for the last year.
"Achieving what I did just now, the sky's the limit," he said. "There's no way I'm going to limit myself."
(Editing by Ed Osmond/Greg Stutchbury)
