Their then 12-year-old son's rectum was ruptured and he suffered severe intestinal injuries.
The parents are claiming R700 000 damages from the department following his 2011 ordeal.
The Gauteng High Court, Pretoria, ordered the department to make an interim payment towards the boy’s medical costs.
The rest of the damages due to the parents will we determined on November 30.
The boy attended a special needs school where most of the pupils displayed behavioural problems.
According to court papers, the teacher, who was supervising the class, stepped out at about noon on November 17, 2011.
He left the class unsupervised while he knew that the pupils exhibited behavioural problems and had access to equipment which could harm someone.
A group of Grade 6 to 8 pupils assaulted the boy when the teacher left.
It is stated that they grabbed him by his arm and violently bent him forward over a table.
They pressed the compressor pipe, which they found in the classroom, into his anus and pumped air at a high pressure into him.
He lost consciousness and was rushed to the Middelburg Hospital, where an emergency operation was performed on him.
He spent four days in intensive care.
His parents said he had to undergo trauma counselling and he would have to undergo further medical treatment.