The council overwhelmingly passed the resolution Tuesday, citing the city's growing Muslim population and the fact that the system observes comparable Jewish and Christian holidays.
But Bloomberg has spoken out against the measure, saying the school year will get too short if the calendar includes too many holidays.
Now it's unclear whether the proposal will become policy, as the council does not have direct authority over the school year -- yet Bloomberg just relinquished control of the school system to a newly appointed board of education.
"Right now the degree of control the mayor has over the education system is completely unclear," said Councilman G. Oliver Koppell, the only council member to vote against the resolution Tuesday.
Bloomberg could still block the measure. Though the city just reappointed its board of education, the state Senate could take action soon to hand Bloomberg back the reins.
Bloomberg predicted as much Wednesday, saying the new board would "serve until Albany rectifies its inaction and reauthorizes mayoral control."
And the new city school board is considered to be largely aligned with Bloomberg anyway.
Koppell, who sides with Bloomberg, said he's concerned that the calendar change would only benefit a relatively small fraction of the student body at the expense of the school year.
"If we accommodate every group's wishes to have off on religious days, we'll have a huge number of days on which kids are off from school," he said. "This is a slippery slope which we'll be going down. ... In my view, the school year's too short as it is."
But advocates are trying to ensure the two holidays get added to the calendar one way or another.
The resolution takes a two-track approach. It calls both for the New York City Department of Education to add on the holidays and for the state legislature to pass legislation amending education law so that the holidays are recognized in New York City schools.
According to a council aide, the state action would trump any action by the city.
The council, in its resolution, cited statistics from the Coalition for Muslim School Holidays showing about 12 percent of New York City public school students are Muslim.
The addition of the holidays to the school year would not be unprecedented. Several New Jersey cities, as well as Dearborn, Mich., have done the same.
The resolution said that adding those holidays "would serve as an important embodiment of ... tolerance and acceptance."
The holidays are Eid Ul-Fitr, which marks the end of Ramadan, and Eid Ul-Adha, which celebrates the willingness of Ibrahim -- known as Abraham to Christians and Jews -- to sacrifice his son. It is the most important Islamic holiday.
The Associated Press contributed to this report.