The Bloemfontein sprinter ran a time of 44.11s during the third of four heats in his last meet on South African soil before heading over season.
The unofficial time stood at 43.88s over the distance, which would have seen him comfortably beat Grenada’s Kirani James to the fastest time for the year. James clocked 44.08s on 29 April in Des Moines, Iowa.
Van Nierkerk has been tipped to break his own South African record this weekend, and if his time on Friday morning is anything to go by, his personal best of 43.38s, he set during the final of the 2015 IAAF World Championships in Beijing will be in serious jeopardy.
Last year the South African Sportsman of the Year for 2015, Van Niekerk, set the time to beat James and the USA’s LeShawn Merritt for the gold medal.
Van Nierkerk will be running in the 400m final on Saturday afternoon at 13:15.