The China Meteorological Administration said the tornado struck about 3pm in the Baiyun district of Guangzhou, a sprawling metropolis and manufacturing centre near Hong Kong.
Videos posted online showed a mid-afternoon sky darkened by storm clouds and debris swirling up into the air.
Authorities said that another 33 people were injured and 141 factory buildings were damaged, the official Xinhua News Agency said.
Tornado warnings were issued for other parts of Guangzhou and there were unconfirmed reports that a second tornado appeared to have hit another district in the city later in the afternoon.
US treasury secretary Janet Yellen visited Guangzhou during an official visit to China earlier this month.
The city, formerly known as Canton, also recently held the Canton Fair, a major export and import exhibition that draws buyers from around the world.
In September, two tornadoes killed 10 people in Jiangsu province in eastern China.
