The regulation passed Thursday puts a 16-ounce size limit on cups and bottles of non-diet soda, sweetened teas and other calorie-packed beverages.
CBS New York reported the vote was approved Thursday with eight in favor and one in abstention.
The ban will apply in restaurants, fast-food chains, movie and Broadway theaters, workplace cafeterias and most other places selling prepared food that fall under the Board of Health's regulation. People who buy sugary drinks at such establishments will still have an option to purchase an additional beverage.
Exempt from the ban are sugary drinks sold at supermarkets or most convenience stores and alcohol and dairy-based beverages sold at New York City eateries.
City health officials say the ban is necessary to combat a deadly obesity epidemic.
The restaurant and beverage industries have assailed the plan as misguided. They say the city's health experts are exaggerating the role sugary beverages have played in making Americans fat.
Some medical professionals applauded the ban.
"For the past several years, I've seen the number of children and adults struggling with obesity skyrocket, putting them at early risk of diabetes, heart disease, and cancer," Dr. Steven Safyer, President and CEO of Montefiore Medical Center, said in an emailed statement. "This policy is a great step in the battle to turn this health crisis around."
Some New Yorkers, however, have ridiculed the rule as a gross government intrusion.
"This is not the end," Eliot Hoff, spokesman for New Yorkers for Beverage Choices, said in a statement. "We are exploring legal options, and all other avenues available to us. We will continue to voice our opposition to this ban and fight for the right of New Yorkers to make their own choices."