Meteorologists from the Severe Weather and Information Service (Swaicsa) have confirmed a cut-off low system hovering over the west of the subcontinent.
This is expected to affect Namibia and the western parts of South Africa, from Thursday into Saturday.
Rains have battered most parts of the highveld, resulting in dangerous driving conditions on main roads in Polokwane, including the N1, R71 and Polokwane CBD.
Three men died on the scene, from a lightning strike, in Polokwane City Centre on Wednesday afternoon.
Similarly, lightning struck a palm tree at a residential complex in Montana, North of Pretoria.
Further down in Pretoria North, rains led to a traffic jam, in areas like Wonderboom and Paul Kruger at Die Poort.
The SA Women’s cricket match was cancelled against Ireland, on Wednesday, as rains turned the pitch into a pool of water.
Residents of the Vaal reported a full Vaaldam with 2 sluices open on Wednesday.
Significant flooding was also reported in the Clayville area, and the Gauteng Provincial Joint Operating Committee (JOC) advised motorists to avoid the area.
The South African Weather Service (SAWS) has warned against severe thunderstorms (at level 2), over the central and eastern parts of the Northern Cape as well as the western parts of Free State.
Damaging winds and waves are expected along the coast between Hamburg and Port Edward.