The city says that 94% of public employees are now vaccinated, including 91% of the police department and 94% of the fire department.
Fewer than 10 employees will be disciplined for their unvaccinated status, officials say.
After first serving a week-long unpaid suspension those workers have the option to test twice a week, according to an agreement.
Those employees will be allowed to work on a staggered schedule to avoid negative impacts on city services.
If city workers aren't vaccinated by Dec. 31, they can face disciplinary measures up to termination.
San Jose mandated vaccination for employees in August following a surge in Delta variant infections.