The city's disaster operations centre said informal settlements, including the major township of Khayelitsha, had been particularly affected by flooding.
Nearly 7,000 structures across Cape Town, including homes and shacks, were damaged, impacting more than 8,000 people, the Western Cape provincial government said.
Days of bad weather had damaged around 14,000 structures across the province, affecting about 15,000 people, it said.
A man died after he slipped on the pavement of a flooded road and fell into a canal on the outskirts of Cape Town, police said.
Several roads, including major highways, were flooded and there were concerns about rising water levels at dams.
An AFP correspondent saw several houses that had lost their roofs in strong winds that also bent power lines, with electricity outages reported in several areas.
Cape Town resident Sammy Gelord said the wind ripped off his roof in the Wynberg suburb.
"I never saw something like that in my life -- it just took the roof and everything," he told AFP.
In Khayelitsha, some residents used spades and buckets to remove water flooding their homes.
"The water is coming in, not (from) on top, just under. So I must ask children to help me to get the water out of the house," pensioner Sonneta Kupido told AFP.
Schools across the city and other parts of the province were ordered to close Thursday because of severe weather warnings in place until Friday. Schools in the Cape Winelands and Overberg areas were told to stay shut on Friday.
A salvage operation was underway up the West Coast from Cape Town after a Panama-flagged cargo ship ran aground Tuesday, having been abandoned by its 18 Filipino crew members as it listed excessively in rough seas.
Provincial authorities said there was no risk of an oil spill. The vessel was carrying fertiliser, the South African Maritime Safety Authority said.
The South African Weather Service warned that "disruptive rain leading to flooding and possible mudslides" were expected for Cape Town as well as the Drakenstein and Stellenbosch areas beyond the city.
Several cold fronts have battered the region over the past few days, with mountainous areas experiencing rare heavy snowfalls. Authorities reported at the weekend that the extreme weather had left hundreds of people homeless.
The Western Cape provincial government said more than 40,000 meals were provided to those in need. It appealed for donations of food, blankets, and toiletries and to national authorities for emergency aid.
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