The Olympic champion suffered the injury while playing a charity touch rugby game in October 2017 and has not raced internationally since.
The South African made a winning return to action in a provincial Free State championships in Bloemfontein in February after almost 17 months out.
The 27-year-old recently returned to training after enduring a number of setbacks, but having been ruled out of last year's Commonwealth Games in Australia, he misses the championships in Qatar as a precaution.
I am a clean athlete, says Hassan
South Africa’s Wayde Van Niekerk will be expected to compete in London in the summer. (Jonathan Brady/PA)
Image credit: PA Sport
"I'm positive and taking things day by day," van Niekerk said in a statement.
I am respecting all the calls made by the doctor and respecting my body. For me it is about listening to my body and taking it from there.
"For now, I am not rushing myself or putting pressure on myself. I'm extremely happy and at peace with where I am."
The world and Olympic 400m record holder had his sights on a third straight world title in Qatar after being handed a wildcard for the event.
Ramil Guliyev a devancé Wayde Van Niekerk pour l'or
Image credit: Getty Images
His doctor Louis Holtzhausen, who has been leading Van Niekerk’s recovery over the last two years, believes it will move more rapidly in the coming months.
"The medical teams, both in Bloemfontein and Aspetar (Qatar), did all we could to have him ready for the World Championships, but it was just not possible," Holtzhausen said.
However, he has successfully returned to track training and all indications are that he will recover more rapidly from now on.
Van Niekerk had hoped to run at the South African championships in April but pulled out and also skipped a proposed return at the London Diamond League in July after suffering a bruise on the bone in his knee.
Van Niekerk beat Michael Johnson’s 17-year world record in the 400-m at the 2016 Olympics and was set to take on the 200-m as well before his injury.