Mr Scipione said it was the actions of "extremist offenders" who turned a peaceful protest violent on Saturday, leaving six police and 17 others injured.
"To see a young child with a placard thrust in his hand calling for the beheading of a person is simply something I cannot comprehend.
"It's just not what we teach our children."
The protest later moved down George Street and to the US consulate in Martin Place, before erupting in Hyde Park where protesters clashed with up to 150 police officers.
Mr Scipione said while some were there to protest lawfully, a few people were determined to make trouble.
"You don't wear a balaclava, you don't wear a face-covering unless you're going to get up to badness and we saw plenty of those in the crowd," he said.
"They were there and they became extremist offenders."
The commissioner said he had "no doubt" that social media played a major role in inciting the violence.
NSW Police on Sunday established Strike Force McAllister, comprising officers from the Central and Southwest metropolitan regions and the State Crime Command.
The group will analyse the footage of the protest provided by the media and will prosecute anyone seen to be committing a crime.
"This is a no-nonsense engagement," Mr Scipione said.
"If you want to act like you are extremist criminals, we will treat you like you're extremist criminals."
Six men have so far been charged with offences including assaulting police and animal cruelty.
Two of the officers who were taken to hospital with head injuries suffered during the melee have been discharged after treatment.
Mr Scipione insisted police were well-prepared for any follow-up protests or "stupid" retaliatory attacks.