Olympic Games and world 400-metre champion
"Successful op done and dusted. Rehab already started. Ready for the hard work ahead," tweeted the 25-year-old star.
His agent, Peet van Zyl, said in a statement: "We are pleased to have received positive news from the doctor, who says the operation went well.
"Wayde had his first rebab session on Wednesday and it went well."
Van Niekerk suffered multiple knee tears last month playing in a celebrities' touch rugby match, one of the curtain-raisers to a South Africa-New Zealand Test in Cape Town.
The South African will undergo rehabilitation in Colorado town Vail, where the surgery was performed, and also in Qatar and South Africa.
He could be sidelined for nine months and among events he is certain to miss is the 2018 Commonwealth Games on the Australian Gold Coast.
Van Niekerk won 400m gold at the 2016 Rio Olympics in 43.03 seconds, smashing a world record set by American Michael Johnson in 1999.
He is the only athlete to run the 100m in under 10 seconds, the 200m in under 20 seconds and the 400m in under 44 seconds.
The South African had planned to compete in the 100m, 200m and 400m at the Commonwealth Games.