In the densely populated capital, rescuers were deployed across the city to help evacuate people from low-lying homes after downpours turned streets into rivers.
People clutched flimsy umbrellas as they waded through thigh-deep murky water or used small boats and shopping trolleys to move around.
Government offices were shut and classes suspended, while more than 70 domestic and international flights were cancelled because of the weather.
"Many areas are flooded so we have rescuers deployed all over the city. There is an overwhelming number of people asking for help," Peachy de Leon, a disaster official in suburban Manila, told AFP.
"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."
Typhoon Gaemi, which has swept past the Philippines as it heads towards Taiwan, intensified the southwest monsoon rains typical for this time of year, the state weather forecaster said.
"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," senior weather specialist Glaiza Escullar told AFP.
More than 200 millimetres (nearly eight inches) of rain fell in the capital in the past 24 hours, Escullar said, which was "not unusual".
Landslides killed a pregnant woman and three children in Batangas province, south of Manila, and blocked three major roads in the mountainous Benguet province, police and disaster officials said Wednesday.
That takes the death toll from heavy rains over swaths of the country in the past two weeks to at least 12, as tens of thousands sheltered in evacuation centres.
