This rules him out of the Trieste Meet scheduled for today.
The 28-year-old was supposed to race the 100m and 400m events in what was his first competition outside of South Africa since 2017.
Van Niekerk has been in quarantine since July 19, the day he landed in Italy from a special flight Johannesburg-Amsterdam-Venice.
He flew with a group of 7 people, including fellow South African athletes Ruswahl Samaai and Antonio Alkana, headed for Gemona del Friuli, where his training camp for the European season is based.
His manager Peet van Zyl was shocked, telling Gazzetta, "I don't know how it is possible. Wayde has been training for the whole week and never had any symptom, not even after testing positive. He hasn't had a fever."
"In the last 14 days each of us has been tested 4 times," van Zyl continued, "the last one was on Thursday. This afternoon (yesterday) we asked to be tested again, we want to make sure to be safe and we are waiting for the results."
The positive rules out a return to the track for the South African 400m specialist who has had a number of setbacks since winning gold at Rio 2016.
Taking Tokyo 2020 postponement in his stride
"We've always been isolated," continued Van Zyl, "we've never been with other people, we have a hotel floor just for us, a dedicated room for breakfast, lunch, dinner."
"We've always avoided any form of aggregation, we only left the hotel to go to the track. This is why we asked for another test, we want to understand."
Van Niekerk did not race in 2018 after he ruptured right knee ligaments during a celebrity touch rugby game in October.
He needed surgery to repair the anterior cruciate ligament tear.
“I am hungrier than before” - Wayde van Niekerk
Then came coronavirus cancellation and Olympic postponement, but he sees the silver lining.
So what happens now?
Van Niekerk will have to isolate for 14 days and take further coronavirus tests until he is clear and tests negatively before returning to race.
It's another setback, but the South African has become accustomed to overcoming adversity.