The rollbacks take effect Sunday and San Francisco Mayor London Breed urged residents to protect themselves and their families.
"Every single person needs to do what they can over the next few weeks. The decisions you make today will impact where we are tomorrow. Do not travel, stay with the people in your household, and wear your masks."
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On Monday, the two counties will also fall under Gov. Gavin Newsom's curfew order for counties in the purple tier. The monthlong partial stay-at-home order requires non-essential work and gatherings to cease from 10 p.m. to 5 a.m.
"It's a further setback and it's a reminder that this pandemic is going to be a long haul for San Francisco," said Rodney Fong, CEO of the SF Chamber of Commerce.
Houses of worship must close for indoor gatherings, but outdoor services are still allowed. The San Francisco archdiocese sent out a statement saying in part: "The government is demoting worship to the same status as watching a movie 'non-essential' but worship is both a natural and a constitutional right."
Indoor operations at museums, aquariums, and zoos, indoor movie theaters, indoor gyms and fitness centers will all be shuttered. San Francisco will also close outdoor carousels, ferris wheels, and train rides.
"It's very disappointing at the same time the safety of our visitors and staff is the top priority," said Thomas Campbell, CEO of the Fine Arts Museums of San Francisco.
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The Fine Arts Museums of San Francisco is having to contact thousands to postpone their visit.
"20,000 tickets, advanced tickets. People bought their tickets online and we have their emails so logistically it takes time but obviously we will honor all of those," said Campbell.
Retail stores must limit capacity to 25%, but outdoor dining is permitted. Indoor retail and indoor personal services, such as hair and nail salons, outdoor fitness and limited indoor one-on-one personal
training at gyms or fitness centers may continue.
Giovanni Cea was managing a busy Saturday lunch crowd at Crepevine restaurant on Burlingame Avenue. News that San Mateo County will move to purple tier Monday, means no more indoor dining.
"It's going to be hard for restaurants to survive, it's going to be cold and we wait for the rain," said Cea.
WATCH: San Mateo businesses react to no more indoor dining, reduced capacity
'It's a total bummer': San Mateo Co. moves back to purple tier
Anki Moletic owns Loft, she knows retail shops like hers will be required to further reduce the number of customers inside, just as the holiday season is beginning.
"Not happy about it, but we'll obey and do what what we need to do," said Moletic. "We'll hope this will go away soon right?"
Those who rely on a paycheck from their retail jobs, now worry what happens next.
"It's not going to be a pleasant thought that my hours could be cut, to counter something equally important," said Divya from San Mateo County.
MAP: CA counties that can, can't reopen under new rules
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Outdoor playgrounds, skate parks (with a 25% capacity limit up to 25 people at a time), batting cages and mini golf, as well as outdoor zoos and art or museum exhibits may remain open.
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San Francisco's troubling numbers show the city averaging 130 new COVID-19 positive cases per day, compared to the 73 per day during the first week of November, Breed said. The city has an estimated 900 COVID-19 cases diagnosed per week -- compared to 217 diagnosed COVID-19 cases the week of Oct. 12.
Last week, San Francisco was the only urban area in the state to avoid being in the purple tier. Today it is 51 of 58 counties at the "widespread" maximum risk level, officials said.
San Mateo County Supervisor David Canepa said, "It wasn't totally unexpected but it's a total bummer."
Canepa says everyone need double down on efforts to flatten the curve.
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In San Mateo County, the health department reported an 85% spike in new COVID-19 cases from October to November. The county's new adjusted case rate is 7.6 per 100,000 population, officials said Saturday.
"We have not seen numbers like this in quite a while and we really need to reverse this incredibly troubling trend," San Mateo County Manager Mike Callagy said. "What's important to remember is that we can reverse the trend as long as we follow common-sense health and safety practices."
"We need to make sure we're still doing the things we've been doing, wearing the damn mask, social distance and washing our hands," Canepa said.
In San Francisco, all schools already open for in-person learning may continue to offer indoor instruction. Under the purple tier, TK-6 schools that have not yet opened, may apply for a waiver from the health officer to open for indoor in-person instruction. Middle schools and high schools that have not yet opened may not open for indoor instruction, however they may apply to provide outdoor-only learning.
Bay City News contributed to this report.
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