Athletics SA president Aleck Skhosana told Netwerk24 that Magakwe refused to give testers a urine sample on December 22 last year.
It was considered a doping violation and the world athletics governing body IAAF has suspended him for two years.
Magakwe (28) is the current South African 100m record holder, with a personal best of 9:98 seconds.
Not only did he break the magical barrier but he also smashed the South African record of 10.06 seconds that he shared with Johan Rossouw.
That record had been part of South African sprinting since 1988 and has been the bane of many a athlete who tried and failed to break it.