Houses, roads, bridges in Surigao del Norte province and a school in Surigao city were damaged, with blackouts also experienced.
The casualties occurred in Surigao del Norte province on the northern tip of Mindanao island which was closest to the epicentre of the quake, which struck at 10.03pm.
MALACAÑANG advised Saturday residents of Surigao City to remain alert for potential aftershocks from Friday night's 6.7 magnitude quake.
A report by Caraga Regional Disaster Risk Reduction and Management Council showed that three people, including a four-year-old boy, were confirmed dead while about 87 were injured.
The Philippines is part of the so-called Pacific Ring of Fire, where earthquakes and eruptions are frequent due to intense seismic activity.
The tremor was felt also felt at Intensity 2 in Bislig, Surigao Del Sur and at Intensity 1 in the cities of Cebu and Cagayan de Oro City.
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Philippine Institute of Seismology and Volcanology said, almost 100 aftershocks have been felt.
The quake has damaged buildings and an airport, and the power has been knocked out, they added.
An injured woman is accompanied by family members at a hospital in Surigao City, early Saturday.
Jim Sydiongco, Civil Aviation Authority of the Philippines (CAAP) director general, on Saturday issued a notice to airmen that the Surigao airport would be shut until repairs are completed.
Most of injured were hurt by falling objects at the height of the quake that delivered more than 100 aftershocks since Friday evening, with magnitudes ranging from 2.0 to 3.7. Investigators said 21 attacks took place in the western German state of North Rhine-Westphalia, which is the country's most populous state with a high number of Muslim immigrants.