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The 26-year-old suffered freak knee injuries during a celebrity touch rugby match in Cape Town two years ago and his rehabilitation included time in the United States, Qatar and South Africa.
Van Niekerk won a 400m race at the provincial Free State championships in central city Bloemfontein in a time of 47:28 seconds, 4:25 sec outside his world record.
South African international hurdler Cornel Fredericks made most of the running against a slow-starting Van Niekerk, who caught up in the final 100m to cross the line first.
It was the first time Van Niekerk had competed since defending his 400m title and finishing second in the 200m final at the 2017 world championships in London.
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The Cape Town-born athlete set the world record of 43:03 when winning 400m gold at the 2016 Rio Olympic Games.