The defending 400m champion won comfortably in the one-lap final, winding down on the home straight ahead of his 200m semi-final on Wednesday (9.55pm SA time).
Van Niekerk completed the race in 43,98, covering the distance 0,43 ahead of Bahamas sprinter Steven Gardiner.
Athletics South Africa President Aleck Skhosana offered congratulations to Van Niekerk on winning gold and sent well wishes as he attempts the double.
“Congratulations to Wayde van Niekerk for retaining the title he won at the 2015 IAAF World Championships in Beijing,” said Skhosana.
“He will put behind his achievement and focus on the forthcoming 200m semi-finals and final in order to achieve his ambition of doubling in the 400m and 200m.
“We thank the coach and the entire team who supported him throughout the rounds and preparing him to stay focused in order to win a gold medal for SA.”
After six days of competition, Team SA team had secured four medals (two gold, one silver and one bronze) and moved to third position on the medals table.
– News24 Wire