Protestors reportedly threw stones at officers and overturned a patrol vehicle in what police chief called a "very grave incident".
Police responded with stun grenades and tear gas, before making several arrests
The clashes have provoked intense criticism from across the political spectrum.
National Security Minister Itamar Ben-Gvir "unequivocally condemned" the "extremist" rioting, calling attacking police a "red line".
Opposition politicians, though, primarily blamed the government, claiming that ministers have been too lax on the issue of Charedi conscription due to the coalition's dependence on the support of the major Charedi parties - Shas and United Torah Judaism.
Yisrael Beytenu Chairman Avigdor Liberman said: "This is what happens when the country’s leadership is in the pocket of Charedi wheeler-dealers."
Likewise, Democrat Chair Yair Golan added: "The draft dodgers understand that the law in Israel does not apply to them.
"The backing for [draft] evasion, and for violence against security forces, comes from above. The prime minister and defence minister are responsible for these shocking scenes.
"It is time to draft everyone and restore law and order in Israel, for the sake of Israel’s security."
The government has recently heavily revised its bill regulating Charedi conscription after the initial draft nearly caused the withdrawal of the Charedi parties from the coalition.
The new version has seen the requirement for full-time yeshiva students to serve excised and the sanctions against draft dodgers softened.
