The area is in the midst of a blistering heatwave - now in its second week.
Smoke blanketed the city of San Francisco as firefighters battled to keep the fires under control.
"Throughout the state of California right now, we are stretched thin for crews" said Will Powers, a state fire spokesperson. He said air resources were similarly limited.
Police and firefighters went door-to-door early on Wednesday in a frantic scramble to warn residents to evacuate as fire encroached on Vacaville - a city of about 100,000 that lies between San Francisco and Sacramento.
Fire officials said at least 50 structures were destroyed and 50 damaged, while four people were injured.
Television footage showed some homes in flames and thick ash dropping in a rural area as the fire appeared to head towards more densely populated areas.
Diane Bustos told KPIX-TV that she and her husband tried to drive out but their vehicle caught fire and they had to flee on foot.
"I got all these flames on me and I lost my shoe, but I made it. God saved me," she said.
The California Department of Forestry and Fire Protection said the blaze was exhibiting "extreme fire behaviour" and challenging firefighters.
To the south in San Mateo and Santa Cruz counties, about 22,000 people were ordered to evacuate because of a fire that was burning in dense wooded parkland.
Thousands of homes and businesses were also threatened in the wine-growing counties of Napa and Sonoma in an area devastated by a series of deadly blazes in the past three years.
Blazes engulfed rural and forest areas near the San Francisco Bay Area, near Salinas in Monterey County, around Oroville Dam north of Sacramento, forested areas west of Silicon Valley, in remote Mendocino County and near the Nevada state line north of Lake Tahoe.
Several were also burning in northern coastline areas and in southern California.
Governor Gavin Newsom ordered a statewide state of emergency on Tuesday.
The cluster of wine country fires threaten an area that only last year grappled with another massive blaze that forced 200,000 to flee – a task made more complicated this year because of the pandemic.
On Tuesday afternoon, the fire was moving towards an area called Atlas Peak that burned in 2017 - a blaze that killed six people and destroyed nearly 800 buildings.
To the south, evacuations were ordered for all of Boulder Creek to the west of Silicon Valley - a community of 5,000 high in the Santa Cruz mountains where windy, long, forested roads, some paved, some dirt, can easily become blocked during storms or fires.