The activists were trying to destroy the family home of the Palestinian gunman who was shot dead after a killing spree at the library of a Jewish seminary. The attack was one of the worst to hit the city in four years.
The activists managed to throw stones at the home in Jabel Mukaber, but caused little damage as police arrested 22 people in the clashes. Two police officers were injured.
Police managed to restore order, although ultra-nationalist leaders threatened the area, home to some 250,000 Arabs, with further protests.
"This is only the beginning. This is the opening shot for a much more complicated struggle against our enemies. We are fed up with the fact that Jewish blood is abandoned and that the prime minister doesn't care. The rage is erupting and leads to the incidents and anger we saw at the village," Itamar Ben-Gvir, who led the protest, was cited by the Ynet news agency.