The protests brought central Jerusalem to a standstill as a group of religious parents prepared to go to prison for defying a court order demanding their daughters attend classes with girls of different ethnic origin.
Parents of European, or Ashkenazi, origin do not want their daughters to be educated in the same classroom as schoolgirls of Middle Eastern and North African descent, or Sephardim, claiming that they are not as religious.
The row brings into sharp focus growing discrimination within religious Jewish communities, and the increasing influence of the ultra-Orthodox sects that have long considered themselves unfettered by society's norms.
Batting off accusations of racism, the parents, who live in the West Bank settler community of Immanuel, have argued that their wish to separate their children is motivated only by religious and cultural differences between the different Jewish communities.
"The Sephardic Jews are less observant, they dress differently," said Carter Schwartz, a 31-year-old protester with an American accent. "It's like sending kids of a totally different learning level to Harvard, and the government forces [Harvard] to take them in."
Israel's Supreme Court has rejected the parents' argument, and has ordered them to serve two weeks in jail.
A massive police presence was stationed around Jerusalem's Old City as 100,000 protesters, both Ashkenazi and Sephardic, converged there to protest the court's decision and proclaim religious rule. A smaller contingent of some 20,000 marched earlier in Bnei Brak, a town near Tel Aviv.
Schoolchildren and women thronged the streets and leaned over balconies overlooking Jerusalem's religious Mea Shearim neighbourhood to watch the mostly-male demonstrators, most of them singing mournful dirges, go past.
Dressed in their traditional black garb and wide-rimmed hats, bearded marchers held aloft banners saying "God will rule for all eternity", a reference to the supremacy of religious interests over secular law, and "High Court against the people".
Many secular Israelis have little patience for Haredi Jews, the extremely conservative, religious minority that lives in ghetto-style communities across Israel, but are concentrated in Jerusalem within reach of Judaism's holiest sites.
Miriam Wiedler, a retired teacher, said that the state was meddling in affairs that should be the sole preserve of the parents, many of whose families pre-date the state. "These Haredim have been in Jerusalem for the last 250 years. They were here when the Turks were here, even before Israel became a state," she said. "If they let everybody live their own lives, nobody would fight each other."
The 43 sets of parents were scheduled to start their prison sentences at midday yesterday. That was later moved to 5pm to allow them to take part in the march and present themselves at a police station in central Jerusalem.
Commentators from both sides of the political divide railed against the marchers, warning that the religious communities have gone too far. "The discrimination in Immanuel contains in a nutshell the essence of the clash between the rule of law and separatist interest groups," wrote the liberal Ha'aretz newspaper in an editorial.
"Such groups... demand state funds to strengthen the independent education system that serves their children, but are unwilling to give in on even a single convention that governs their lifestyle."
The Haredi Jews are seen as an economic drain on society, with many of the men choosing years of subsidised religious studies over paid employment. A soaring birth rate has led to predictions that they could form a majority of Jerusalem's half-million population in a decade.
In recent months, they have proved a disruptive presence, littering Jerusalem with rubbish and soiled nappies to protest against a new parking lot that would encourage more traffic on the Sabbath and clashing with police to prevent the exhumation of ancient human remains that they claim are Jewish to make way for a new emergency hospital wing.
"No negotiation or agreement are possible with people who have no God but their father in heaven and his representatives on earth," wrote Yossi Sarid, a liberal commentator.
"This is a war... we cannot afford to lose. The rebellious Haredim must be put in their place, so that we, too, have a place in which to live."
At least some of the ultra-Orthodox community withheld their support from yesterday's demonstrations. Rabbi Yuval Sherlo, who heads the army's religious programme in Petah Tikva, called on religious Jews not to take part in the march.
"I cannot take part in the racism and discrimination that is taking place, which is just the tip of the iceberg," said Mr Sherlo, Ha'aretz quoted him as saying. "It's impossible to claim that this is Jewish law or that it is sanctifying the name of God."
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