Israeli nationalists chanted “death to the Arabs”, “may your villages burn” and “Gaza is a graveyard” in a state-sponsored march through Jerusalem to mark the anniversary of the city’s capture and annexation.

The annual assertion of Jewish control over Palestinian East Jerusalem has grown more extreme in recent years, and Thursday’s event culminated with the national security minister, Itamar Ben-Gvir, unfurling an Israeli flag in front of the al-Aqsa mosque, the holiest Islamic site in the city.

Most Palestinians in the Muslim quarter of the Old City had shuttered their shops and gone home before the march began, but members of radical Jewish groups who had entered scuffled with Palestinian residents still there, with both sides throwing chairs at each other, until separated by police who entered the city that afternoon in force.

“I’ve come to show all the world that this is our city. This is the Holy Land. God gave us this country and this city,” a 19-year-old marcher, Ariel Amichai, said.

Asked what the intended message of the march was to Palestinians in Jerusalem, he replied: “That they must leave. This is our country. And they can’t just be here and try to stab us or kill us.”

Amichai, who is from Modi’in, 43km from Jerusalem, said he believed that Jerusalem Day, marking the capture of the east side of the city in 1967, was the only day when Jews could enter the Muslim quarter through the Damascus Gate, though Israeli Jews and Palestinians use the gate on a daily basis.

Marchers were bused in from around Israel and from settlements in the occupied West Bank in a vast operation funded by the Jerusalem municipality and government ministries. The finance minister, Bezalel Smotrich, also took part in Thursday’s march.

Once Palestinians had left the Old City, much of the tension was between government-backed marchers and members of a Jewish group, Standing Together, which had come to protect Palestinian residents from political violence.

Suf Patishi, a Standing Together organiser, said a record 400 volunteers had turned up in hi-vis vests in the organisation’s trademark purple, on a day fraught with risks.

“We wanted to really cover each and every corner of the city to make sure that we prevent attacks against Palestinians,” Patishi said. “Yes, it is dangerous to us, but nothing like the danger to the Palestinians that are living here.”

There were a few religious Jews among the protective cordon of counter-protesters. An ultra-orthodox man with a long grey beard and gold coat said he had come from northern Israel and gave his name only as David.

“I’ve become appalled by the violent behaviour of people in my community,” David said. “I’m a man of faith, religious, and they’re doing this in our name, and I felt I should do something to contrast that. This is a desecration of God’s name, so the only way to remedy that is to do the opposite, a Kiddush Hashem, a sanctification of God’s name.”

On the al-Aqsa compound, known to Jews as the Temple Mount, Ben-Gvir danced with supporters singing “the Temple Mount is in our hands”, as he unfurled an Israeli flag. The national security minister has led a campaign to erode the 59-year status quo, dating back to the Israeli capture of East Jerusalem and the West Bank, under which non-Muslims are forbidden from praying in the sacred area.

On Thursday evening, Ben-Gvir wrote on his Telegram social media account: “59 years after the liberation of Jerusalem, I raised the Israeli flag on the Temple Mount and we can proudly say: We have returned governance to the Temple Mount.”