Weather authorities lowered the typhoon signal in the Asian financial hub on Sunday afternoon - to eight from the maximum of 10, after more than 110mm of rain fell within three hours.
Much of the rain concentrated on the northern region neighbouring the mainland, the city's observatory said, warning of more to come.
The government said in a statement 26 people sought treatment in public hospitals, while 253 flocked to its shelters, and 471 fallen trees were reported.
In North Point near the city's harbour, large swathes of scaffolding were swept off a residential building and onto the road.
As Wipha tracks westward across the South China Sea, it is expected to make landfall later on Sunday between Zhuhai and Zhanjiang in the southern province of Guangdong, state-run broadcaster CCTV said.
Authorities in neighbouring Macau, the world's biggest gambling hub, also downgraded the typhoon signal to eight from 10, warning of flooding in its inner harbour area and urging residents to stay safe, public broadcaster TDM said.
Hong Kong's airport authority said 80,000 travellers were hit by the rescheduling of 400 flights forced by the typhoon.
Cathay Pacific Airways cancelled all flights from Hong Kong airport on Sunday, waiving ticket change fees and arranging for rebooking.
Most public transport in Hong Kong was suspended, including ferries, amid high sea swells.
