Residents shared videos of heavy rainfall in Welkom, Boksburg, Krugersdorp West and Limpopo.
There is also a hail storm on the N3 Townhill.
The Johannesburg Roads Agency (JRA) said it identified high-risk flooding hotspots in Johannesburg as Region F, including the inner City, Hillbrow and Johannesburg South.
Heavy rains led to an outage in Mayfield, Chief Luthuli and surrounding areas.
Severe thunderstorms are expected to continue on Wednesday, over the Eastern North West, Gauteng, Western Mpumalanga and South Western areas of Limpopo.
Similar but lesser conditions at Level 1 are also expected in the north-eastern KwaZulu Natal.
Picture: Susara Maria Myburgh, Carletonville.