The quake happened eight miles south of Indios at a depth of six miles at 8.54am local time, the US Geological Survey said.
There were no immediate reports of injuries, although power outages were reported across much of the south and possible damage was being assessed at power plants.
Barbara Cruz, a prosecutor who was in the southern coastal city of Ponce when the latest earthquake hit, said concrete debris hit pavements as buildings crumbled.
She said: "Everyone is out on the street."
The latest tremor is the strongest since a magnitude 6.4 quake – the biggest to hit the island in a century – struck before dawn on Tuesday, leaving thousands of people without power or water.
Victor Huerfano, director of Puerto Rico's Seismic Network, told the Associated Press that he expects more aftershocks.
He said: "It's going to re-energise an unstable situation. It's a complex zone."
Hundreds of tremors, most of them minor, have struck Puerto Rico since the start of the year.
Tuesday's earthquake left at least one person dead and injured nine, triggering a tsunami alert and damaging or destroying thousands of buildings.
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