Eden District Municipality says flare-ups are causing most distress as residents are being urged to evacuate the area.
Emergency services have begun evacuating parts of Knysna in the Western Cape as a massive fire raged late into the evening on Wednesday.
A auto is washed over by a huge wave that slammed into the promenade during heavy storms in the Sea Point neighborhood of Cape Town.
Worst-hit was Knysna, a town of 77,000 people 500 kilometres (310 miles) east of Cape Town on South Africa's famed Garden Route, as firefighters battled to quell 26 fires along the tourist trail.
"Humanitarian support is being co-ordinated for an estimated 8,000 to 10,000 residents of the greater Knysna area, after devastating fires last night", said James-Brent Styan, spokesman for the Western Cape local government ministry.
"Reports of some evacuees heading back to evacuated areas in Knysna is a matter of concern. Now we are trying to make all areas safe and the fire is not under control", Manuel said.
"I'm scared to stay in my house because of wind", Cape Town resident Unati Sigcau said. The weather system which struck on June 6 has damaged buildings, felled trees, left 46,000 homes without electricity and caused travel chaos as flights and rail services were hit by gale-force winds and flooding.
Also on Thursday, President Jacob Zuma extended his deepest condolences to the families of those who lost their lives in the storm that engulfed the Western Cape.
Numerous homes have been gutted by the blaze that started on Tuesday and grew rapidly when a storm passed over the Western Cape town.
Schools which were closed on Wednesday will reopen on Thursday, he said.
While the storm provided some relief for a severe drought, officials said sustained rainfall over several years is needed in a city whose reservoirs are at low levels.
MTN added that it is aware that customers in Cape Town and the Eastern Cape are experiencing intermittent service disruptions due to power lines damaged by strong winds.