Nearly 115,000 people have been affected by the gales, which have hit eight cities since descending on the region on Sunday, Xinhua said.
Two people were killed and 24 injured when a storm brought down a wholesale market building in Foshan city, Guangdong province, the state media agency said.
A strong gale and heavy rain struck the fruit market in Foshan city, Guangdong province, at around 7:00 am (2300 GMT Thursday), Xinhua said, citing local officials.
Three more are missing after falling into flood waters, Xinhua added.
Storms have already caused havoc in the region. Last week, a huge crane collapsed in high winds in Guangdong province, killing 18 people at a construction site.
A further 18 were hospitalised following the accident in the city of Dongguan.
China's meteorological authority forecast torrential rain will hit areas south of the Yangtze River over the course of Saturday.
It has so far given the storms the lowest rating on its four-tier warning system.
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