The earthquake was recorded at 4:48 a.m., according to the USGS.
The area is prone to small quakes, USGS spokeswoman Stephanie Hanna said.
Hanna said she believes the small temblor occurred off the San Andreas Fault. It came on the heels of a magnitude 5.4 quake in Southern California Tuesday but was in no way related, Hanna said.
Bay Area residents are unlikely to feel any aftershocks from the Los Angeles-area quake but Hanna said USGS scientists believe the Hayward Fault is due for another big one.