Weather SA's Elizabeth Webster told News24 that there was a 60% chance of rain for Limpopo on Thursday and it was "unlikely" that the heavy rains would persist.
The service said in almost 48 hours 120mm of rain was measured at Phalaborwa, and 270mm at Hoedspruit.
Skukuza and surrounding areas saw up to 135mm of rainfall in the last 48 hours.
Earlier in the day, the Kruger Park issued an urgent warning that gates and roads have been closed as a result of rainfall.
It said that the Phalaborwa, Crocodile Bridge and Giriyondo border post entrance gates have been closed.
Biyamiti Bush Camp, Shimuwini Bush Camp, Talamati Bush Camp and Tshokwane picnic site have also been closed.
The Tinga Private Lodge and guests on the Sweni Wilderness Trail were evacuated. The SANParks helicopter was used for evacuations where necessary.
Meanwhile, the Weather SA warned that a heatwave would continue in the Western Cape. Temperatures in the Cape Winelands went up to 40°C on Tuesday while the West Coast Redelinghuys sizzled in the 42°C heat.
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