The quake struck at 4:23 am at a depth of 41 kilometres (25 miles) off Mindanao island, the US Geological Service said.
Residents were jolted from their beds and ran onto the streets as the earthquake shook the area, leaving cracks in a hospital, two government buildings and a port, as well as triggering the collapse of at least one house and causing a brief power outage.
"The floor appeared to rise first before swaying violently from side to side. Then the lights went out," said Adrian Morallas, who was at work at the civil defence office in General Santos city at the time of the quake.
"I ducked and took cover under my desk in line with our disaster training, though it was very difficult to do that in the dark with the ground shaking."
Mr Morallas said coastal communities near General Santos were told to evacuate as a precaution, though authorities do not know how many people actually left their homes.
The state-run Philippine Institute of Volcanology and Seismology gave a higher magnitude reading of 7.2. The epicentre was about 53 kilometres off Mindanao's south coast, it added.
Mr Morallas said two people were injured during the evacuations in the Mindanao coastal towns of Glan and Malapatan.
One person was hit by a falling rock while a pregnant woman hurt herself when she fell.
Philippine Institute of Volcanology and Seismology chief Renato Solidum said that residents near coastal areas in the region should be wary of possible tsunami waves.
The Philippines lies on the so-called Ring of Fire, a vast Pacific Ocean region where many of Earth's quakes and volcanic eruptions occur.
A 6.0-magnitude earthquake damaged dozens of houses on central Mindanao on April 12, while a trio of strong quakes battered buildings and caused panicked tourists to flee a popular resort near Manila on April 8.
A 6.5-magnitude quake killed eight people and left more than 250 injured outside the Mindanao city of Surigao in February, and another 5.9-magnitude tremor killed one person there last month.
Before Surigao, the last lethal earthquake to hit the country was a 7.1-magnitude tremor that left more than 220 people dead and destroyed historic churches when it struck the central islands in October 2013.
(With inputs from AFP and IANS)