"The system will pose a great risk for the next 36 to 48 hours, particularly in terms of further exceptionally heavy rainfall and resultant flooding", the South African Weather Service said in a statement.
Tropical storm Dineo has left a path of destruction in its wake along the coast of Mozambique since it arrived yesterday.
Strong winds and rain is seen in and around Inhambane, Mozambique as Cyclone Dineo move through the area.
The projected maximum strength of surface winds associated is about 130km/h, slightly weaker than earlier estimates of 160 to 170km/h.
The storm‚ which was downgraded from a tropical cyclone on Thursday morning‚ is expected to bring as much as 200mm of rain in 24 hours to parts of the country.
The interaction with the land of Mozambique is expected to continue weakening the storm as it tracks further inland on February 16.
"These communities are already extremely vulnerable due to the impacts of prolonged drought".
He warned that southern Mozambique would experience "very heavy rainfall‚ most likely in the region of 100 to 200mm per day‚ or even more".
Dineo was expected to dissipate in the region of Musina and Beit Bridge on Friday and drift towards Botswana by Saturday.
A warning for severe thunderstorms was in effect over the south-western parts of the Waterberg District of Limpopo with possible heavy rain leading to localized flooding as well as large amounts of small hail.
As the lower portion of the Limpopo River flows directly through the Mozambican region, it is most likely to be severely affected.
Tropical storms and cyclones‚ which originate over open water‚ weaken significantly as they pass over land.