Gov. Andrew Cuomo won’t be able to penalize New York City for failing to adopt teacher evaluations while a lawsuit against the penalty makes its way through the courts, a State Supreme Court judge ruled today.

The judge said Cuomo’s latest ultimatum — that the city adopt a system or have one imposed — proved that a financial penalty was not the only way to motivate districts to adopt new evaluations.

Cuomo announced last year that he would withhold increases in state school aid from districts that did not adopt new teacher evaluation systems by Jan. 17. New York City missed the deadline, and Cuomo said he would take back $250 million from the city’s schools.

But parents and advocates of equitable school funding sued, and a judge today issued an injunction against the penalty, at least until he has had more time to consider the merits of the lawsuit.

City officials praised the ruling, as did other advocates of teacher evaluations who have usually supported Cuomo’s efforts to strong-arm districts into adopting new evaluation systems.

“We’ve said all along that students should not be penalized for the UFT’s failure to negotiate, and our goal has been and continues to be a fair and effective evaluation system,” said Deputy Mayor Howard Wolfson.

UFT officials declined to comment immediately but said they were reviewing the decision.

Cuomo’s office plans to appeal the ruling, according to a spokesman. The State Education Department — whose commissioner, John King, is also named in the lawsuit — declined to comment on the ruling.

To win a temporary injunction at the outset of a lawsuit, plaintiffs have to prove that allowing a process to continue while litigation is underway would cause “irreparable harm.” They also have to convince the judge that they are likely to win the case in the end.

Those requirements are why lawyers for the state and for the parents wrangled over the value of $250 million to the city’s schools , during a hearing last week. Michael Rebell, the attorney who filed the lawsuit, argued that the penalty violated students’ right to a sound basic education, which the state’s school aid formula is meant to support. But lawyers for the state argued that the size of the penalty — 4 percent of the city’s schools budget — would barely make a dent in students’ educational experiences.

Judge Manuel Mendez sided with Rebell and the parents. “Innocent students that had no influence over the legislative process or [teacher evaluation] negotiations were potentially placed at risk academically,” he wrote in his decision.

Mendez also used Cuomo’s latest strategy to get the city to adopt new teacher evaluations — seeking the right to let King impose an evaluation system if one is not agreed upon by June 1 — as evidence against the governor. Cuomo has said one reason to impose an evaluation system is to make sure the state’s federal Race to the Top funds, which were contingent on new evaluations, are not threatened.

“There are alternative means of achieving [evaluation] goals while preserving federal RTTT grant funds without the long term effects of financial sanctions on students,” Mendez wrote.

“While this is only the first round in what may be a long fight, we remain hopeful that the funds will be permanently returned to the students and teachers who need them,” said Jonathan Schleifer, executive director of Educators 4 Excellence, which has strongly supported Cuomo’s push for new evaluations.

Another supporter of new evaluations, Mona Davids, founder of the New York City Parents Union, said the ruling was a vindication of parents’ ability to stand up for students.

“It’s important because parents stood up on our own and fought against the governor and have at this point stopped him from punishing our kids for the failure of the city and teachers union to reach an evaluations agreement,” said Davids, who was one of several parents to join the suit. Robert Jackson, chair of the City Council’s education committee, is also a plaintiff.

Mendez’s ruling in favor of an injunction is below.