The city had vowed an appeal and said Thursday that lawyers had filed it late Monday.
In his decision on March 11, State Supreme Court Justice Milton Tingling said the 16-ounce limit on sodas and other sweet drinks arbitrarily applies to only some sugary beverages and some places that sell them.
"The loopholes in this rule effectively defeat the stated purpose of this rule," Tingling wrote in his ruling, which was seen as a victory for the beverage industry, restaurants and other business groups that called the ban unfair.
In addition, the judge said the Mayor Michael Bloomberg-appointed Board of Health intruded on the City Council's authority when it imposed the rule.
In its appeal, the city disputed those points.
"The rule is designed to make consumption of large amounts of sugary drinks a conscious and informed choice by the consumer," it said. "Thus, although a consumer is free to consume more than 16 ounces by ordering a second drink, getting a refill, or going to another store, he or she will be making an informed choice."
The city also said the Board of Health had legislative authority, and "is empowered to issue substantive rules and standards in public health."
Said American Beverage Association spokesman Christopher Gindlesperger, referring to the initial decision overturning the ban, "We feel the justice's decision was strong and we're confident in the ruling."
Also on Thursday, the city announced that other organizations had filed legal briefs in support of the city's appeal. Those organizations include the National Alliance for Hispanic Health and the National Association of Local Boards of Health, as well as 30 others.
Bloomberg has made public health a cornerstone of his administration, from requiring calorie counts to be posted on menus and barring trans fats in restaurant foods.