That is similar to the phase-out period allowed when California eliminated personal belief vaccine exemptions in 2015, officials said.
Another new provision could revoke any medical exemptions written by Robert Sears, a Southern California doctor who has been disciplined by the Medical Board of California for writing an improper vaccine exemption.
The provision would apply to exemptions written by any doctor who has faced disciplinary action, but at this time Sears is the only California doctor to be disciplined regarding vaccine exemptions, said Carlos Villatoro, a medical board spokesman.
Sears told The Los Angeles Times it would result in hundreds of his patients losing their exemptions.
"This seems like a broad overreach from a government that is supposed to protect its medically fragile children," he said.
Other changes would make it clear that enforcement will start next year, meaning doctors who previously granted a high number of medical exemptions won't face scrutiny.
They also would remove a requirement that doctors swear under penalty of perjury that they are not charging fees to fill out medical exemption forms. And one change would ensure that an expert panel reviewing appeals of exemption denials could consider additional information from the doctor beyond the exemption form.
Newsom spokesman Nathan Click said the governor would sign the bill once the new amendments have also won legislative approval.
"These amendments clarify legal and administrative processes in SB276 in order to ensure medical providers, parents, school administrators and public health officials know the rules of the road once it takes effect," Click said in a statement, referencing the bill number.
Newsom's 11th-hour demands had roiled the Legislature and frustrated the bill's supporters, all of whom were caught by surprise when he announced them in a tweet this week.