It was the strongest to hit the Bay Area since 1989, when a quake struck during the World Series.
Sunday's earthquake struck 4 miles northwest of American Canyon, 6 miles southwest of Napa, and 9 miles southeast of Sonoma, according to the USGS.
CNN affiliate KTVU reported a church in Vallejo was heavily damaged and lost its bell tower.
There were no immediate reports of injuries.
The USGS estimated, based on their locations, that 15,000 people experienced severe shaking, 106,000 people felt very strong shaking, 176,000 felt strong shaking, and 738,000 felt moderate shaking.
Napa County Fire Capt. Jim Christenson said units were driving around looking for damage.
A dispatcher for the Napa County Sheriff's Office said there was some water damage.
Pacific Gas and Electric Company reported outages for more than 5,000 customers in and around Sonoma, Napa, and Santa Rosa.