Two classrooms and two offices were burnt down in the fire on Thursday, said Sadtu, which distanced itself from the act.
It said the teachers were demanding the appointment of their own preferred candidate for principal.
"The recruitment process of school-based educators is conducted in terms of relevant legislation and policies which provide for grievance procedures," Sadtu said in a statement.
"The burning of a school deprives children of the poor and the working class a golden and much needed opportunity to participate in the quality learning and teaching campaign as adopted by the organisation."
Sadtu said it would take disciplinary measures against any of its members found to be involved.
Gauteng education department spokesperson Phumla Sekhonyane said due process was followed in the appointment.
"The school governing body made recommendations, which is provided for in legislation, and the department accepted that recommendation," she said.
Sekhonyane said the legislation also allowed for appeals against the appointment, but that so far there had been none.
She said the department could not comment on the fire as investigations were ongoing.
"Authorities are investigating the cause of the fire. At this stage it is too early to speculate on the cause of the fire and the extent of the damage," she said.
Pupils were sent home on Thursday in the interest of their safety, but were allowed back on Friday. The damaged sections of the building had been cordoned off while the forensic investigation was done, she said.