It follows a 6.4 magnitude quake Tuesday that killed one person, knocked out electric power and caused widespread damage.
The U.S. Geological Survey said the 8:54 a.m. ET quake hit 13 kilometres south of Indios at a shallow depth of 10 kilometres.
The USGS revised its initial report of a 6.0 magnitude quake to 5.9.
Puerto Rico was hit with a 5.9-magnitude quake on Saturday morning, the latest in a tumultuous few weeks of seismic activity that has rocked the island.
Randy Baldwin, a geophysicist at the U.S. Geological Survey, said the 6.0-magnitude natural disaster is just one of many aftershocks that occurred with several 5.0-magnitude aftershocks overnight.
The island's power authority said Saturday's quake left an estimated 5,000 customers without power.
The quake, just off the U.S. territory's southern Caribbean coastline, was felt throughout much of the island, including the capital San Juan.
The director of Puerto Rico's Electric Power Authority, ordered the temporary closure of the company's largest plant, which crews had been inspecting for damage caused by earlier quakes.
That storm killed nearly 3,000 people, and left millions of Americans without power, water or shelter.
Puerto Rico Governor Wanda Vazquez declared a state of emergency after Tuesday's quake, which forced an automatic shutdown of the power grid.
More than 6,000 people were staying in shelters, Rep. Jenniffer González-Colón, the territory's non-voting delegate to Congress, said Friday. "If you've been displaced or are helping with relief efforts, you can book free accommodations between January 9, 2020 and January 31, 2020".