Shallow floods, damaged shanties and ripped off tin roofs were a common sight across the region on Monday, but there was no major destruction after Hagupit slammed into Eastern Samar and other island provinces.
Hagupit still had maximum sustained winds of 120-km per hour and gusts of 150-kph on Monday, considerably weaker than its peak power but still a potentially deadly storm, according to forecasters.
The typhoon, which made landfall in Eastern Samar late on Saturday, was moving slowly, dumping heavy rain. It is likely to head into the South China Sea later on Tuesday.
Al Jazeera's Andrew Thomas, reporting from the city of Batangas, said that while the typhoon had not been as destructive, there were still concerns that the rainfall could trigger landslides and flash floods.
He reported that most government offices, schools and private businesses in Manila remained shut.
Traumatised by the death and destruction from Typhoon Haiyan last year, more than a million people fled to more than 1,000 emergency shelters and safer grounds as Hagupit approached.
Manila Mayor Joseph Estrada said more than 3,000 residents of a shantytown on the edge of Manila Bay had been evacuated due to possible storm surges.
Metropolitan Manila has a population of more than 12 million people.
Two people, including a baby girl, died of hypothermia in central Iloilo province on Saturday at the height of the typhoon, disaster-response agency chief Alexander Pama told a news conference.
Another person died after being hit by a falling tree in the eastern town of Dolores, where the typhoon first made landfall, according to Interior Secretary Mar Roxas.
"The low number of casualties is a testament to the amount of preparation," Thomas said.
Displaced villagers were asked to return home from emergency shelters in provinces where the danger posed by the typhoon had waned, including Albay, where more than half a million people were advised to leave evacuation sites.
Nearly 12,000 villagers, however, will remain in government shelters in Albay because their homes lie near the restive Mayon volcano.