Van Niekerk picked up medial and lateral tears of the meniscus, as well as a torn anterior cruciate ligament (ACL), which foreced him to undergo surgery to his right knee at the Steadman Clinic in Vail, Colorado.
In a statement released last night, Van Niekerk said he would undergo rehabilitation for six months in Vail, Doha and South Africa.
This means that he will miss out on participating at next year's Commonwealth Games in Gold Coast, Australia in April.
"I was looking forward to competing in the 100m and 200m events in Gold Coast, and participating at the national championships in March, so this is unfortunate timing," Van Niekerk said in a release.
"But this is sport and these things happen. I trust that the team I have around me, including the medical professionals, will make this process as smooth as possible."
The South African sensation's season had already been cut short due to a niggling back injury after winning double medals at the IAAF World Championships in London in August.
Van Niekerk successfully defended his 400m world title and added the 200m silver medal to his growing list of accolades.
He had since set his sights on racing the 100m-200m double at the Commonwealth Games, where he would also have been available for the 4x100m relay.
Van Niekerk was hopeful of a speedy recovery and that he would be able to compete next year following intense rehabilitation.
"I have faith that, God-willing, I'll be able to race again later next year," Van Niekerk said.
"Full recovery is going to be crucial, so I'll be patient, but I will work as hard as I can to get back on the track as soon as possible."
