Rains from Tropical Storm Trami fell across the city of nearly more than 12 million people throughout the night and continued today morning.
Schools in provinces outside of Manila were also closed, a government statement said, as the heavy rain pounded a large area of the main island of Luzon.
The statement said all government offices in Manila were also closed, while the Philippine Stock Exchange announced it would not open.
Waist-deep water in some parts of Manila made roads and highways unpassable.
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There were no reports of fatalities.
In the mountainous north of Luzon, 200 people were evacuated from their homes to avoid landslides, according to the government's disaster agency.
Heavy rain is forecast to fall across Manila and Luzon throughout today.