Typhoon Hato made landfall at noon on Wednesday near Zhuhai city in Guangdong province, bringing with it strong winds and lashing rain.
Hong Kong raised its typhoon warning signal to 10, the highest level. The territory and nearby Macau were brought to a standstill.
The storm caused widespread flooding, blackouts and destruction.
Chinese state media said nearly 27,000 people on the mainland were evacuated.
Authorities have issued alerts for landslides, flooding and other geological disasters, reported Xinhua.
Hong Kong 's meteorological authority said Hato had maximum winds of up to 175kph (109mph).
Eight people were killed in Macau, while four were reported dead in mainland China. Another person remains unaccounted for, according to local media.
Businesses, schools, train stations and airports were forced to shut on Wednesday, with only one aeroplane managing to land at Hong Kong's normally busy airport, the South China Morning Post reported.
The storm is estimated to have cost the global financial centre up to HK$8bn (£800m; $1bn).
Hato, which means "pigeon" in Japanese, is still making its way westwards inland but is losing power, according to Hong Kong authorities.