The quake struck at 7.37am on Monday and registered a magnitude of 7.8, according to the Philippine Institute of Volcanology and Seismology (Phivolcs).
The tremor's epicentre was located southwest of Maasim town in Sarangani province, on the southern island of Mindanao, Phivolcs said.
Four people remain missing and a total of 144 were injured, according to official figures.
Thirty-one of the fatalities were from the Sarangani region, General Santos City and South Cotabato while four were from the Davao region.
The tremor was also felt in parts of Indonesia, particularly on the island of Sulawesi where a tsunami warning was also issued.
Japan likewise warned parts of its Pacific coastline of possible waves.
The US Geological Survey lifted its tsunami warning later on Monday.
It also reported numerous aftershocks.
The agency had previously warned that waves of up to three metres could occur along some coastal areas.
The Philippines' Phivolcs has since also lifted its tsunami warning, after reporting waves of up to 1.5 metres in six coastal areas.
In eastern parts of Indonesia, the Meteorology, Climatology, and Geophysical Agency (BMKG) recorded small tsunami waves at several monitoring stations.
However, the sea level rose only slightly in this area, the agency said, also lifting its tsunami warning.
Meanwhile, the extent of the damage in the region remains unclear.
Videos circulating on social media showed several buildings collapsing or partially collapsing in the Mindanao region.
Electricity and telecommunications services were disrupted in affected areas, the Philippine's disaster agency said.
School classes were cancelled while work in government and private offices was also suspended.
The earthquake struck on the first day of the school year, during flag-raising ceremonies at schools and government offices, meaning many students, teachers and staff were already outside buildings.
Elene Marie Jane Gamboa, principal of Matanao National High School in Davao del Sur province, said one of the school buildings collapsed.
"Thank God we were having our flag-raising ceremony and everyone was outside," she told Manila radio station DZMM.
Philippine President Ferdinand Marcos Jr immediately ordered relief and protective measures and called on the population to follow the instructions of authorities.
Mindanao region lies on the Pacific Ring of Fire, a belt of intense tectonic activity encircling the Pacific Ocean, where earthquakes and volcanic eruptions occur with particular frequency.
