The midfielder was admitted to hospital after his black BMW collided with a mini-bus taxi between Maraisburg and Soweto at 05h00, but his injuries are not believed to be life-threatening.
He will remain in hospital for at least two days as doctors assess his injuries, though.
A female passenger in the BMW was seriously injured, however, after she had to be freed from the wreckage by rescue services.
Three people, including a pregnant woman, were also injured in the taxi.
Although she would not comment on the cause of the accident, Metro police Inspector Edna Mamonyane says authorities had opened a case of reckless and negligent driving against Khumalo.
The 40-year-old starred for Chiefs between 1987 and 2002, though he did also play in Turkey and the United States during that period.
He also made 50 appearances for Bafana Bafana, scoring the very first goal on the nation's return to international football from isolation - a penalty against Cameroon in a 1-0 win in 1992.