The court heard footage was passed to Merseyside Police after undercover reporter Sasha Hinde spent seven weeks as an employee at the school in Wallasey leading up to May.
Sentencing Millar, District Judge James Hatton said: "This is a serious, but I accept unusual, case because it was brought to light by an investigation by an undercover reporter.
"One can only speculate if that investigation had not occurred whether the behaviour demonstrated in this case may well have carried on unabated."
The footage showing Millar drawing on the boy's face was played to the court and a woman, described as management, was seen to walk past.
In a statement read to the court, the victim said he had been "embarrassed" in front of his classmates.
Judge Hatton said: "It would be obvious to anyone that your conduct was hideously inappropriate and nothing short of cruel bullying.
"You were clearly in a position of trust. One case involved you drawing a penis onto the face of a pupil.
"That involved gratuitous degradation of your victim."
He put two pupils into headlocks and also feigned a punch and kick at one of them, the court heard.
In a statement, the family of one of the three boys assaulted by Millar said: "Even though he was mistreated badly, he thought it was the norm."
Millar was also charged with common assault against Ms Hinde in the staffroom as he reenacted something which had happened.
Anthony Nelson, defending, said Millar had ADHD and was "utterly inappropriate" for his role at the school.
He said: "He was interviewed by the principal very informally and started work the next day and had no training or guidance.
"It does not excuse his conduct, but perhaps explains it."
He said the behaviour was "endemic" and "the norm" at the school, which has closed since the documentary aired.
Millar, of Bradman Close, Liscard, Wirral, pleaded guilty at an earlier hearing to two counts of common assault, two counts of assault by beating and using threatening and abusive words or behaviour likely to cause harassment, alarm or distress.