The four counties -- along with the city of Berkeley, which operates its own public health department -- said that their local indoor mask requirements will no longer have exceptions as of 12:01 a.m. Thursday.
"Everyone, regardless of vaccination status, must wear a mask in all indoor public settings," said Ted Appel, a Sonoma County spokesperson.
Health officials in the five jurisdictions cited rising local case counts and the emergence of the highly contagious omicron variant as reasons to align with the state's blanket indoor mask mandate, which runs through at least Jan. 15.
"We've seen a growth in breakthrough cases among vaccinated people, nearly 80 cases a day are now being detected in Sonoma County among people who are fully vaccinated, that's an all time high," Appel told KRCB Wednesday afternoon. "And we're aware of at least two COVID outbreak following holiday parties where stable cohorts of fully vaccinated people gathered indoors without wearing their mask and resulted in nearly 40 known positive cases so far."
"The omicron variant requires us to use all the tools at hand to reduce the chance of transmission," Berkeley Health Officer Dr. Lisa Hernandez said. "Masks are more important than ever to minimize the spread of COVID to our most medically vulnerable community members."
Masks have been required indoors, regardless of vaccination status, in Berkeley and seven Bay Area counties, including Sonoma, Marin, San Francisco and Alameda, since early August amid the onset of the delta variant.
In early October, the four counties, the city of Berkeley and Contra Costa County allowed fully vaccinated people to remove their masks indoors in small settings that are not open to the general public like offices, fitness classes, occupational vehicles, religious gatherings and college classes.
Contra Costa County rescinded their masking exceptions on Tuesday.
Health officials across the region touted lower case rates when making those exceptions to their local masking orders in early October.
On Wednesday, officials in multiple counties said their case rates are reaching their highest levels in months.
According to Marin County, 338 new cases of COVID-19 were reported on Tuesday, more than 100 cases higher than the county's previous highest one-day case count.
Marin County Public Health Officer Dr. Matt Willis said the region's surge in cases tied to omicron necessitated a response.
"The mask exemption for certain settings was a pre-omicron policy," Willis said in a statement. "This variant behaves differently, and the risk of infection in a room full of vaccinated people who are unmasked is much higher now."
In addition to rescinding its mask mandate exemptions, San Francisco announced that it will formally align with the state's requirement that workers in health care settings get a COVID-19 booster vaccination by Feb. 1, 2022, if they are eligible.
The city will also require that workers in high-risk settings, who are not covered by the state's booster requirement, get a booster by Feb. 1 as well.
"As COVID-19 becomes endemic, we need to ensure everyone eligible gets vaccinated and boosted, we sustain our hospital capacity, and protect the most vulnerable -- these updates to the Health Order help us achieve that," San Francisco Director of Public Health Dr. Grant Colfax said in a statement.
Health officials in all five jurisdictions called on residents to get vaccinated against the virus if they have yet to do so, or to get a booster dose if they are eligible.
Booster vaccines are recommended for people age 16 and up who got their second Pfizer or Moderna vaccine dose at least six months ago or those who got their single Johnson & Johnson vaccine at least two months ago.
KRCB's Greta Mart contributed to this story.