The patient showed symptoms of the respiratory illness, which is caused by the coronavirus, and the doctor referred him to hospital, where he tested positive.
Dr Nadina Wessels told TimesLIVE on Monday that the patient was treated at her practice in the suburb of Heidedal on April 2.
As a precaution, Wessels said she was in self-isolation at home and her practice had been closed pending her test results.
However, she said she had no symptoms.
On Sunday, health minister Zweli Mkhize announced that the country had 1,655 confirmed Covid-19 cases. Of those, 87 were in the Free State.