The 3.3-magnitude tremor struck just before 5am on Monday at a depth of about 3.5 miles (6km), the USGS said.
The closest town to the earthquake was Alamo, California, about two miles away.
No injuries have been reported and it is understood there has been no structural damage.
The East Bay area was also hit with several small earthquakes on Sunday, USGS said.
On 18 April, the USGS released a fact sheet about what would happen in the event of a major earthquake in the San Francisco Bay area.
The fact sheet, named “The HayWired Earthquake Scenario – We Can Outsmart Disaster”, looks at earthquake hazard impacts, mitigation efforts, and resiliency actions for communities.
Ken Hudnut, one of the lead authors of the report, said: “The USGS and its partners have worked together to anticipate the impacts of a hypothetical magnitude-7.0 earthquake on the Hayward Fault, before it happens, so that people can use the latest science in their efforts to become even better prepared.”
The Hayward Fault is a zone in California’s San Francisco Bay which is at risk of tremors.
It runs through densely populated areas, including Berkeley, Oakland, San Leandro, Hayward and San Jose.
In geological terms, a fault is a crack in the Earth’s crust, which makes the area more likely to experience earthquakes as the cracks shift.
USGS scientists describe the Hayward Fault as a “tectonic time bomb”.
The last major earthquake along the Hayward Fault on 21 October 1868 killed 30 people and caused around $350,000 worth of damage.
Scientists believe another major tremor could hit the area at any time.