A teacher who bounced in and out of the “rubber room” for five years over misconduct charges at a notoriously violent Harlem middle school had her fine slashed by $5,000 yesterday by a state appeals court.

In 2011, the Department of Education slapped Julianne Polito, of the now-shuttered MS 344 Academy of Collaborative Education, with a $7,500 fine after she was found guilty of throwing a book at a special-education student and saying, “Here, Mr. Smarty Pants, let’s see if you can read.”

Polito, 59, a tenured teacher with 18 years of experience, sued the city, claiming the department’s hearing officer relied on faulty testimony from the student, who had serious developmental disabilities.

Yesterday, Polito’s fine was reduced to $2,500 because her “remark, although improper, was not of a highly inflammatory nature and her actions appear to constitute an isolated incident,” the court found.

A Law Department spokesman was “disappointed.”