The quake, which was centered two miles south of Vallejo, occurred at 9:13 a.m. On Wednesday, a 3.5-magnitude temblor occurred at 6:09 p.m. three miles south of Vallejo, according to the USGS.
Sue Simon, the assistant to the Vallejo city attorney, said she felt both.
"It was a small jolt then a big jolt," Simon said of this morning's quake.
She said the jolts were about a half-second apart, and that she felt them from City Hall.
"I was told the large windows in the building flexed out a little," Simon said.
The USGS has received responses from throughout the Bay Area about the quake, most of them from the cities of Vallejo, Benicia, Napa, American Canyon and Martinez.
Richard Allen, director of the Seismological Laboratory at the University of California at Berkeley, said he felt the "weak shaking" this morning that lasted a less than a second.
He said it occurred close to the continuation of the West Napa Fault, which runs east of Santa Rosa southeast to Vallejo and is parallel to the Rodgers Creek and Hayward faults.
Because both quakes were of magnitude 3.5, he considers them a cluster. If this morning's quake had been of a lesser magnitude, it would be considered an aftershock, Allen said. Both quakes had a depth of 5.7 miles, Allen said.
Clusters are not that unusual, Allen said, noting that there were three or four small quakes in Berkeley in October.