At least 100 officers, on foot and on horseback, were stationed at a protest in Sydney's inner east on Tuesday evening.
It came after violent clashes between demonstrators and police 24 hours earlier which resulted in the arrest of 27 people.
Nine people, aged 19 to 67, were charged with offences including behaving in an offensive manner in a public place and resisting police.
Police are issuing an additional six protesters with court attendance notices for failing to comply with move-on directions.
Videos posted on social media from the event showed a man with raised hands being punched repeatedly in the stomach by officers, while another depicted a group of Muslim men praying before being ripped from their knees and taken away by police.
Five members of the public were hospitalised.
There was a sense of anger at Tuesday's protest, with goggle-wearing demonstrators chanting anti-police and anti-government slogans.
Mr Herzog should never have been invited to Australia, Palestine Action Group spokesman Josh Lees told the rally.
"In order to roll out the red carpet for him they crushed the rights of the people in this city to protest against him. We absolutely will not be intimidated," he said.
Tuesday's protest came after the city bore witness to "a very dark night" that included "unprovoked violence and aggression" from police, Australia's special envoy to combat Islamophobia Aftab Malik said.
NSW Police Commissioner Mal Lanyon described the assembly on Monday as a "volatile" crowd.
Premier Chris Minns defended the actions of police and pointed to strong relations between authorities and the Muslim community.
"NSW Police have had a strong and co-operative relationship with Sydney's Islamic and Arabic community, going back decades," he said.
"But context is important and the circumstances facing police were incredibly difficult ... it was in effect in the middle of a riot."
Mr Minns criticised his MPs who attended Monday's rally and called out some speakers for attempting to march despite police restrictions.
Labor MP Sarah Kaine, who spoke at the rally, rejected any suggestion she had incited violence.
Greens MP Abigail Boyd said her assault by three police officers dispelled notions the response was proportionate.
"I got this almighty shove from my right and I went flying, lifted off the ground ... and then this one copper just punched me as I was trying to get my balance," she told AAP just hours after returning from hospital.
"I only weigh 60kg, I'm only five foot three, I don't understand why they were attacking me. I'd said I was a member of parliament.
"I've never seen anything like it, it was so brutal."
Officers restricted movement along most of the boundary of the demonstration site, forcing the large group into a gridlock.
Police issued a move-on order but the situation escalated as the densely packed crowd struggled to leave before officers rushed at protesters in an attempt to disperse the group.
Community worker Paula Abood said she was assaulted by police on two occasions while trying to help other rally-goers who were being hit.
"I've never seen anything like this in my 40 years of marching the streets of Sydney," she said.
Mr Herzog was invited to Australia after the Bondi terrorist attack.
He has faced scrutiny over 2023 comments which a UN inquiry found might reasonably have been interpreted as inciting genocide against Palestinians.
The president denies that claim and says his comments were taken out of context.
