Lesley Cooper was alleged to have called the boy at St Duthus School in Tain a "puppy", whistled at him and told him to "sit".
A General Teaching Council for Scotland panel said three pupil support assistants had "colluded in fabricating a false complaint" against Ms Cooper.
A temporary restriction order on the teacher has been removed.
Highland Council-run St Duthus School caters or pupils with severe, complex and profound additional support needs.
A hearing held into the allegations against Ms Cooper heard claims that she had been frustrated by the behaviour of the boy.
It was alleged the teacher repeatedly acted in an inappropriate manner and used excessive force. It was allegedly that she told the pupil: "You're going to be my puppy".
The panel heard evidence from teaching staff, including the head teacher, and Vivienne Fraser, Fiona Smith and Kirsty Bonthrone, the pupil support assistants (PSAs) who made the complaint.
The PSAs claimed that their input on handling pupils would be overruled leading to the atmosphere between them and teaching staff becoming "tense".
In a newly-released outcome following the hearing, the panel said it rejected the evidence of the PSAs about the alleged conduct of Ms Cooper.
The panel said: "Far from demonstrating that a teacher had acted deplorably in a relation to a young pupil with additional support needs, the panel found that the evidence showed that a group of PSAs mounted a sustained campaign of harassment and vilification against the teaching staff at the school to the extent that it caused the suspension of the Head Teacher and the respondent by Highland Council.
"The panel heard evidence that members of the core group of PSAs were responsible for undermining the teaching plans and instructions of the teachers and that this extended more recently to supply teachers."
A teacher has been cleared of accusations that she mistreated a pupil at a Highland school.