The south-east Asian nation's disaster agency revised its death toll to 45 from 72 after checking reports from ground staff, including rescue workers searching for 18 missing persons.
Residents in the capital's coastal area were evacuated while classes across all levels were suspended, according to the mayor's office.
Manila Mayor Honey Lacuna-Pangan ordered the closure of the city's cemeteries on Saturday, where millions had been expected to visit during the extended All Saints' Day weekend.
The tropical storm, which has maximum sustained winds of 95 kilometres per hour and gusts of up to 130kph, made landfall in the eastern Philippines on Saturday.
The state weather agency gave warnings of widespread flooding and landslides because of heavy and at times torrential rains over the capital region and nearby provinces as Nalgae cuts through the main Luzon island and heads to the South China Sea.
Airlines have cancelled 116 domestic and international flights to and from the Philippines' main gateway. Nearly 7,500 passengers, drivers, and cargo helpers and 107 vessels were stranded in ports, the coast guard said.
Government agencies were giving aid and food packs to affected families, President Ferdinand Marcos Jr said on Twitter.
Coast guard personnel guided residents through chest-deep floods, with rescuers using a monobloc plastic chair and an old refrigerator to carry children and elderly people in the central Leyte province, according to photos shared by the agency.
The bulk of the deaths have been reported in the southern Maguindanao province.
"We are not discounting the possibility of more casualties," Cyrus Torrena, provincial administrator of Maguindanao, told DZMM radio station. "But we pray it does not go up significantly."
The Philippines records an average of 20 tropical storms annually. In December, Typhoon Rai, a Category 5 storm, ravaged central provinces, killing 407 and injuring more than 1,100.