The city council unanimously approved the ban Tuesday night following a heated public hearing last week.
The vote comes the same day state health officials approved an emergency ban on flavored e-cigarettes making New York the first state in the country to do so.
Some residents are worried about lung illnesses tied to vaping while small business owners worry the move will cause them to go out of business.
The Yonkers ban will take effect on Oct. 1. Meantime, retailers across the state now have two weeks to remove the products from store shelves.