Andrew Porter, aged 32, from Alford, Aberdeenshire, who said he was rescuing a colleague pinned down on the floor by the pupil, was fired as learning support teacher at Oakbank School in Aberdeen for gross misconduct, even though he refuted the complaint.
An Aberdeen employment tribunal strongly criticised the "inconsistent and contradictory" evidence gathered by the school authorities to justify the sacking. The school is now considering whether to appeal.
The tribunal heard that pupils at Oakbank were often traumatised and could present disturbing and challenging behaviour.
The 15-year-old boy had left the class without permission and Mr Porter had been escorting him along the corridor when the pupil kicked him. It was then that Mr Porter, assisted by another teacher, Gordon Smith, restrained the pupil. Another pupil pulled Mr Porter away.
The first pupil overcame Mr Smith and held him on the ground with his arm around his neck.
Mr Porter returned and shouted at the pupil several times to let him go. It was only when he did not do so that he took hold of the pupil's arm and began to pull him away from his colleague. He was sacked following an investigation.
On his return from hospital the pupil made a written statement to Jane Arrowsmith, the principal, that the teacher had used excessive force. His arm was in a sling and he claimed it was broken.
Following the incident in March 2000, Mr Porter was suspended pending an investigation. At his disciplinary hearing, he argued there were many inconsistencies in the evidence and it was impossible to conclude his action had been inappropriate or that he had used excessive force.
But Mrs Arrowsmith concluded that Mr Porter had used unnecessary force, used inappropriate physical intervention techniques and, as a result, the pupil suffered a fracture to his left arm.
The tribunal heard Mr Porter had received a written warning for assaulting a pupil in 1996. But this amounted to no more than taking hold of a pupil by the coat after he had been verbally abusive. He appealed to the board of governors against his dismissal but this was unsuccessful.
The tribunal said the evidence the school had gathered was contradictory and inconsistent. It was not at all clear when the boy's arm had been broken.
It considered that the school and, in particular, Mrs Arrowsmith, who took the decision to dismiss, had been selective in the evidence they chose to use.