Two of five charges against Stephen Downes (59) from Glebe Gardens in Moira, were dropped during the final day of the hearing at Lisburn magistrates court.
He was found guilty of two of the other three charges.
The teacher at Parkview Special School denied grabbing and striking a girl after she drank another pupil’s milk and wilfully assaulting another girl when they were alone in a room together, with the door closed on dates between 2010 and 2011.
Judge Rosemary Watters said she was satisfied he had been cruel to the children.
Judge Watters said she “couldn’t think of injured parties any more vulnerable” and did not accept that Downes’ use of the term “fear factor” meant “creating awareness of boundaries”.
Downes will be sentenced for two charges of cruelty against a person under 16 on May 10.
The parents of the two severely disabled girls assaulted by Downes told reporters they had been through hell on their long fight for justice over the past two years.
The mother of one of the girls was reported as saying: “I’m hugely relieved.
“It’s been the most horrible episode at every step of the way.
“Because these children can’t give evidence themselves they have no voice.
“Children at the thinnest end of the wedge deserve protection.
“We want people who work with children and vulnerable adults in care homes, hospitals or schools to know it isn’t okay to treat children like this and at some point there will be someone watching and that person will be prepared to take action.
“And if you can’t treat someone properly in that setting, get another job, go somewhere else.”
The mother of the other girl said her daughter had “suffered badly” as a result of what happened at Parkview.
“I’m glad and relieved this is all over,” she said.
“I am disgusted by what happened and that we had to push so hard to get to this point.
“My daughter couldn’t vocalise what happened to her, but her behaviour changed completely, like bed wetting, and she didn’t want to go to school.
“I knew there was something wrong and thought maybe there was a problem with a pupil.”
Both mothers said they want all parents and everyone who works with children to be listen to what youngsters are telling them and if they notice changes in behaviour not to dismiss it.
Downes’ lawyer, Michael Boyd, indicated his client would be appealing the court’s ruling.