After heated debate, the majority of the state legislature's two chambers voted to pass the measure.
With Governor Andrew Cuomo planning to sign the bill, New York will join a handful of other states, including California, that have banned religious exemptions.
Authorities declared measles eliminated in the United States in 2000, but there have been 1,022 cases reported in the country this year, the worst since 1992.
There are several major hotspots in and around New York -- particularly in areas with large Orthodox Jewish communities such as Brooklyn, which has reported 588 cases since October, and Rockland, which has reported 266 -- that sprang up last fall and threaten the nation's "elimination status."
For weeks, public health experts have called on state legislators to outlaw religious exemptions for vaccines, worried by the growing number of "anti-vaxxer" parents, who have been accused of using religious exemptions as a pretext not to vaccinate their children.
"The fact is that we have a movement against vaccines and we have to confront it with correct information," said Democratic Senator Shelley Mayer.
"We have a public health crisis... I believe the time is right, we have to do the hard thing."
Dozens of legislators voted against the bill, arguing that banning religious exemptions risks violating the First Amendment, which protects religious freedom.
"One of the things that truly distinguishes (this country) and makes us great is the First Amendment. I think this is a step too far and too much an infringement on people's religious beliefs," said Republican Senator Andrew Lanza.
"Asking for an exemption does not mean you get it," he added, noting that authorities could still have denied exemption requests they deemed unjustified.
New York city officials began requiring residents in heavily affected areas to be vaccinated starting in April, but the city still had 173 cases that month and 60 in May.
Schools were also allowed to turn away students who had not been inoculated, but this did not stop the outbreak from growing.
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