The 24-year-old smashed the 400-meter world record held by track and field legend Michael Johnson since 1999, taking the gold ahead of defending champion Kirani James with a time of 43.03 seconds.
And Johnson was quick to congratulate van Niekerk, tweeting: "Congratulations @WaydeDreamer to you and your coach! Well done and deserved. Olympic Gold and World record. I know the feeling!"
Van Niekerk's dominant run was all the more impressive considering he ran in lane eight, with James and American LaShawn Merritt, who took the bronze medal, out of his line of sight for the entire race.
His incredible athleticism is underlined by the fact he's the first man to run under 10 seconds over 100 meters and sub 20 seconds over 200 meters as well as breaking the 44 second barrier over 400 meters.
Van Niekerk's run electrified an Olympic Stadium crowd who arrived expecting fireworks from Bolt but instead left in awe of track and field's newest superstar.
Bolt was quick to congratulate van Niekerk, with the latter revealing he had been inspired by the world's fastest man during a training camp in Jamaica.
"I was over there (Jamaica) for about two weeks training," said van Niekerk. "He's been such a huge rock, inspiring me as an athlete.
"He told me back in Jamaica that 'you will break the world record.' And he came to me after (tonight) and said 'I told you you can do it.'
"These are guys that inspired me -- Usain Bolt, Michael Johnson, I learned from them, and even the guys that ran against me today, Lashawn Merritt, Kirani James, these are guys that inspired me."
Van Niekerk admitted he was surprised to see nobody on his shoulder as he rounded the final bend and it was the absence of his rivals that powered him towards history.
"Yeah, I thought someone was going to catch me, because I felt very alone and I was like 'what's going on, what's going on?'" he said.
"It gave me so much motivation to keep on pushing, keep on pushing, and as I got to the finish line I just dove for the finish line and right after that I said 'don't sit, don't sit', so I went on my knees and thanked the Lord and right after that I went to my family and thanked everyone for tonight."
Van Niekerk lives in South Africa's Free State, according to his page at the International Association of Athletics Federations
, and comes from a family of athletes.
"I just carried on the legacy," he said. "Sport has always been something my family does."
Van Niekerk switched to the 400m in 2012 -- and says he hates the event.
"I hate the 400m but look how far it's brought me," he said. "Once you've been blessed with something you need to use it as best as possible. I'm not going to waste it."
He made the switch after joining his current coach, Ans Botha -- a 74-year-old great-grandmother.