BBC reports the 24-year-old finished in 43.03 seconds, 0.15s quicker than the time Johnson clocked in Seville in 1999.
Grenada's Kirani James, London’s 2012 champion, won the silver medal, with American LaShawn Merritt in bronze.
"Usain Bolt will be retiring soon, this could be the next star," said Johnson who won two Olympic 400m titles.
"He just put those guys away. 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 added Johnson.