The 24-year-old claimed the gold medal on Sunday by clocking 43.03 seconds, beating the previous record held by American Michael Johnson by 15 hundredths of a second, Xinhua reported.
Grenada's Kirani James grabbed silver in 43.76 seconds with the USA's Lashawn Merritt taking bronze in 43.85.
Van Niekerk said he had spent time with seven-time Olympic gold-medallist Bolt in Jamaica earlier this year.
"I was over there for about two weeks training. 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 tonight and said 'I told you you can do it'," Niekerk said.
Johnson's mark had been one of the longest standing records in athletics, having stood since 1999.
Van Niekerk became the second Olympic champion from South Africa in the men's 400m after Bevill Rudd, who achieved the feat in 1920.
-Source IANS