Government offices were shut and classes suspended, while more than 70 domestic and international flights were cancelled because of the weather.
At least 12 people have died from floods and landslides caused by heavy monsoon rains, the national disaster agency said on Wednesday.
“Many areas are flooded so we have rescuers deployed all over the city. There is an overwhelming number of people asking for help,” said Peachy de Leon, a disaster official in suburban Manila.
“We were told last night the rain will not hit us, then the rain suddenly poured so we were quite shocked. There is an ongoing search and rescue now.”
A landslide buried a rural shanty on Tuesday in Agoncillo town in Batangas province, south of Manila, and the bodies of a pregnant woman and three children, ages 9 to 15, were dug out on Wednesday morning, raising the toll in the country to at least 12 dead.
Four of those killed died from landslides in the southern region of Mindanao, while three drowned in floods or swollen rivers.
Landslides also blocked three major roads in the mountainous Benguet province, police and disaster officials said on Wednesday.
“Usually the peak of rainy season is July and August and it so happens that there is a typhoon in the eastern waters of the Philippines that enhances the southwest monsoon,” said senior weather specialist Glaiza Escullar.
More than 200 millimetres (nearly eight inches) of rain fell in the capital in the past 24 hours, Escullar said, which was “not unusual”.
The Philippine archipelago is hit by an average of 20 tropical cyclones every year.
The strongest typhoon to ever hit the Philippines was Super Typhoon Haiyan, which killed 6,300 people and displaced more than 4 million in November 2013.
Additional reporting by Associated Press, dpa