The storm forced President Jacob Zuma, who was in Cape Town, to cancel a speech to an worldwide media conference in Durban, a city on the Indian Ocean coastline, his office said. However, hundreds of homes were flooded or damaged.
Eight people were killed by storms in Cape Town, South Africa, authorities said Wednesday.
One other person was killed when a building collapsed.
With the 2.30pm high tide coinciding with spring tide and forecasts of swells up to 16 metres high‚ residents of coastal areas were warned to move to higher ground if possible.
The BBC's Mo Allie in Cape Town reports that before the storm, there had been several interfaith prayer group meetings praying for rain.
Rainfall is expected over the western parts of the Western Cape and the Northern Cape is expected to see between 20 and 40mm in general, with heavy rainfall exceeding 50mm or more, expected in the mountainous areas.
"By Wednesday afternoon, sea conditions are expected to reach very high seas, with wave heights of between 9m and 12m stretching between Cape Columbine and Cape Agulhas, and then extending north towards Alexander Bay by Wednesday evening as well as into Plettenberg Bay".
It also forced the closure of schools and universities.
The Khayelitsha township, a vast encampment of tightly-packed shacks just outside Cape Town, was reported to be totally deserted except for a handful of children and suffered severe flooding.
That's led to raging fires in the area that have claimed three lives. Now it is the storm. South Africa has been in desperate need of rainfall following two years of water shortages that have resulted in a drought declaration.
The storm hit the Cape Peninsula early on Wednesday morning, which some have described as the "worst storm in living memory".