The family's lawyer, Simon Judd, said the boy's mother was "happy" with the result.
The family said the boy's behaviour during the incident did not amount to gross misconduct, and the school had used the incident as an excuse to remove him from its care.
YouthLaw, which represented the boy's family, said the court clearly found that the school acted illegally when suspending and excluding the pupil and should have taken into account his special needs and recommendations made by his psychologist about managing his behaviour when making those decisions.
"We just hope that our client can be supported to return to mainstream education."
In his decision, Justice Faire said the student was "no ordinary student who has decided to test the boundaries to see how he might deliberately test a teacher's patience, whether to obtain peer accolade or for some other reason", he said.
"'A' is a student with a significant disability which, at times, manifests itself in behavioural problems which include an inability to react when placed in a confrontational position. How he should be handled when placed in such a situation clearly required skill."
The incident that resulted in the boy's suspension happened on July 5, last year.
He struggled with a teacher over a skateboard that he had been riding during class time.
"The incident does appear to have been escalated by the teacher deciding to pursue 'A' and requiring him to give up his skateboard," the judge said.
Justice Faire said he hoped the boy's parents and the school continued to work cooperatively to ensure the student could complete his education.
Costs were reserved.
