The Hong Kong Observatory issued a "red rainstorm warning" as rain pelted down at 50 millimeters (1.97 inches) per hour, drenching the city that has had only one rain-free day this month.
A trough of low pressure over southern China brought 215 millimeters of rain at the observatory between midnight and noon Friday.
Many commuters got to work late as the heavy rainfall caused traffic chaos, with broken down cars blocking major roads and tunnel.
Some 64 flights were delayed by 15 minutes or more, while rough seas caused the cancellation of some ferry services.
Classes at all primary schools were suspended for Friday afternoon.
The downpour came after it rained for all but one of the first 22 days of June and after Hong Kong was drenched by 508.6 millimeters of rain in May, about 200 millimeters above average, an observatory spokesman told AFP.
Some 58 cases of flooding and four landslides were reported across the territory by mid-morning.
Temporary shelters were opened for those in need of accommodation.
The red rainstorm warning was cancelled at 1:30 pm (0530 GMT). The observatory warned of more heavy downpours and thunderstorms over the weekend, although the weather was expected to improve by the middle of next week.
Torrential rains and floods have pounded southern China, leaving 97 people dead and more than 60 missing on the mainland.
The weather in China's south is in sharp contrast with northern China, where a heatwave has sent temperatures soaring above 40 degrees Celsiusdegrees Fahrenheit) in many places.