Motshwari had flu-like symptoms last week and after undergoing tests, his results came back positive.
The player is currently in self-isolation for the next 14 days.
The 29-year-old Motshwari turned professional when he signed with Bidvest Wits in 2014 before he joined Pirates in 2018.
The Bucs central midfielder is the first confirmed case amongst the professional players in South Africa since the coronavirus outbreak in the country.
The Premier Soccer League suspended all fixtures in mid-March, and it is still not clear if the current season will resume anytime soon.
Keep fighting and stay strong Buccaneer!💪
— Mamelodi Sundowns FC (@Masandawana) May 7, 2020
💙| We’d like to wish former #TheCleverBoys midfielder Ben Motshwari a speedy recovery.
— Bidvest Wits (at 🏡) (@BidvestWits) May 7, 2020
— Lamontville Golden Arrows FC (@goldenarrowsfc1) May 7, 2020
— Chippa United FC (@ChippaUnitedFC) May 7, 2020
Get well Ben, you can beat this!❤️ pic.twitter.com/PyNSNTF7v2
— TS Galaxy FC (@TSGALAXYFC) May 7, 2020