Van Niekerk tested positive for the coronavirus in July, disrupting the restart of his season, but returned to win the 400m at the Gala dei Castelli in Switzerland as well as domestic South African meets over 60m and 400m.
Now he is switching his sights to next year, with Tokyo 2020 on the calendar.
"I am far from done," he proclaimed on social media.
The world record holder made his decision on Monday (16 November), announcing that he had decided not to run at a meet in Potchefstroom on Tuesday.
"We know what to focus on now, so we can go back to training and concentrate on preparing for the 2021 season. I look forward to racing again next year."
His agent Peet van Zyl was quoted by EME News as saying: "Wayde feels he would benefit more from going into a tough training block now. He and his coach (Ans Botha) and some of her group will go to a training camp. "
South Africa's national championships are expected to be held in around April.
The 400m heats at the Tokyo 2020 Olympic Games are scheduled to take place on 1 August 2021.