The shallow quake, located far from the coast, hit at 8:02 pm local time (1302 GMT), the USGS said. No tsunami warning has been issued.
Daryono, an official at Indonesia's Meteorological, Climatological and Geophysical Agency (BMKG), said the second quake was one of 23 aftershocks following the earlier one.
"Modelling results showed that this quake does not have potential to cause a tsunami," he said in a statement.
The earlier 7.1 magnitude quake, which hit at 11:53 am, was felt moderately in the town of Saumlaki in the archipelago's Tanimbar Islands, according to BMKG.
"The earthquake was quite intense. But the people here were not panicking. We are used to having earthquakes," Saumlaki resident Lambert Tatang told AFP.
"Especially after we learned that there was no tsunami threat, so life is just normal now," the 41-year-old said.
Indonesia experiences frequent earthquakes due to its position on the Pacific "Ring of Fire", an arc of intense seismic activity that stretches from Japan through Southeast Asia and across the Pacific basin.
In November last year, a shallow 5.6 magnitude quake hit the populous West Java province on the country's main island of Java, killing 602 people.
In 2004, a 9.1 magnitude quake struck the coast of Sumatra and triggered a tsunami that killed 220,000 throughout the region, including about 170,000 in Indonesia.
Comment: Details of the earlier quake: Indonesia's Banda Sea rocked by shallow 7.1 magnitude earthquake