Mayor Michael Bloomberg had made the city's plans clear, but a formal notice was filed Tuesday.
A Manhattan judge said Monday that the rule was arbitrary and outside city health regulators' purview.
It bars eateries from selling non-diet soda and some other sugary beverages in portions bigger than 16 ounces.
Bloomberg calls the ruling a "temporary setback." He says the city is confident it will win an appeal.
The American Beverage Association and other opponents say the judge's ruling is strong.
City officials point to the city's rising obesity rate and studies tying sugary drinks to weight gain. Opponents call the rule unfair and wrong-headed.