Meteorologists at the Hong Kong Observatory said the storm was the most powerful to hit the city since 1979, with sustained gusts of wind recorded at 121mph.
In the Philippines, flooding and landslides were the main causes of death as the toll rose to 65, with 43 injured. In China, four people were killed by either falling trees or building materials in the southern province of Guangdong.
On Monday, Mangkhut weakened to a tropical storm as it moved deeper into southern provinces. It remains on track to pass over the Guangxi regional capital of Nanning and make its way towards the popular tourist destination of Yunnan.
Hong Kong security minister John Lee Ka-chiu had warned residents on Sunday to prepare for the worst as the eye of the storm passed close by.
People were told to stay away from the coastline, while bus, ferry and rail services were suspended and almost 900 flights were cancelled at the city’s busy international airport.
The South China Morning Post said Hong Kong's hospitals had to use backup power due to outages caused by the storm.
Glass windows shattered on commercial skyscrapers, the newspaper reported, while the storm tore scaffolding from buildings under construction and flooded some areas with waist-high water. Officials said more than 200 people were injured.
Resident Elaine Wong said she could feel her high-rise building moving in the storm. "It swayed for quite a long time, at least two hours," she told the Reuters news agency. "It made me feel so dizzy."
By Sunday evening, more than 2.4 million people had been evacuated in China's Guangdong province. In the territory of Macau, the famous casinos were ordered to close due to a typhoon for the first time in history.
But it was the northern Philippines that appeared to have come off worst. Wind speeds were recorded there at up to 127mph, and landslides hit two villages in the mountain province of Benguet.
Most of those reported missing were feared buried in a single incident near the town of Itogon, where dozens of gold miners and their families sought shelter from the storm in an old three-storey chapel.
The building was obliterated when part of a mountain slope collapsed. Three villagers who managed to escape told authorities what happened.
Men used pikes and shovels to dig into the mud looking for survivors, with heavy equipment unable to reach the site. The rescue work was paused overnight and resumed on Monday morning.
"They thought they were really safe there," the mayor of Itogon told the Associated Press. He said there were fears the death toll could rise to more than 100.
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