The charge over the alleged attack on Assyrian church bishop Mar Mari Emmanuel came as officers zero in on as many as 50 people involved in a violent riot after the incident.
NSW Police said counterterrorism officers interviewed the 16-year-old in hospital on Thursday and changed him with committing a terrorist act.
He was refused bail and a bedside court hearing was expected on Friday.
Bishop Emmanuel was stabbed during a live-streamed sermon at Christ the Good Shepherd Church at Wakeley on Monday night.
The attack was declared a terrorist act because of the teen's possible religious motivation.
Dozens of police were injured, their cars vandalised and a cohort of officers and paramedics were forced to shelter inside the place of worship.
Dani Mansour, from Doonside, was the first person arrested and charged over the public-disorder incident.
Stabbing victim Assyrian church bishop Mar Mari Emmanuel (right) says he forgives his attacker. (HANDOUT/CHRIST THE GOOD SHEPHERD CHURCH)
Police told Mansour as he was arrested "the commissioner of police told you we were coming. We are here."
Appearing in court on Thursday, the 19-year-old said he made a mistake but he was "pissed off" at officers who had hurt people outside the church.
Mansour allegedly filmed himself kicking two police cars during the riot before uploading the footage to Instagram.
Speaking to reporters outside Blacktown police station on Thursday, he said he had "just done one (police car)".
NSW Police Commissioner Karen Webb said the man was not a member of the church community.
"(What) has been shown is that people just came along to participate in a riot and that's disgraceful and disgusting," she said.
As many as 50 people were wanted for questioning over the unrest, including several who disguised themselves and police were looking for public help to identify, Ms Webb said.
In an audio message released by the church earlier on Thursday, the bishop said he was doing fine and recovering quickly, while calling on followers to obey the law following the riot.
"I need you to act Christ-like, the lord Jesus never taught us to fight," he said.
Bishop Emmanuel said he forgave the teen allegedly responsible for the stabbing as well as "whoever sent (him) to do this".
Bishop Emmanuel was stabbed at Christ The Good Shepherd Church in western Sydney. (AP PHOTO)
"I forgive whoever has done this act, I say to him, 'You're my son, I love you, and I will always pray for you'," he said.
Bishop Emmanuel's call for calm comes after western Sydney religious leaders also tried to quell community tensions after the attack.
Police declared a terrorist act because the teenager allegedly made comments in Arabic that referred to insults against "my prophet" before stabbing the bishop, who had previously publicly criticised Islam and other religions.
An extra 70 additional officers have been deployed across the region to conduct high-visibility patrols at places of worship.
Another 42 officers have been assigned to investigate the riot, during which some of the crowd tried to gain access to the alleged attacker while he was being held inside the church.
Investigators are collating evidence including mobile phone and CCTV vision to identify those involved.
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