Last week, ultra-orthodox Jews staged one of the biggest protests against the state of Israel.
The women, who were sentenced to two weeks in jail, belong to a strictly observant Ashkenazi sect.
The Ashkenazi parents refused to send their children to school with Jewish Sephardi girls, citing religious grounds as the reason.
Sephardi families are of Middle Eastern or North African origin.
The Ashkenazi parents, who are of European descent, want segregated classrooms because they say the Sephardi families are not religious enough.
The court has exempted 13 of the mothers from jail to care for their children and allowed nine to delay serving their sentences until their jailed husbands returned home.
"These are mothers in special circumstances and they have been allowed to stay at home," a justice official told the AFP news agency.
Some of the women were said to be pregnant or have children with special needs, reports said.
Thousands of ultra-Orthodox Jews had protested against the original court ruling that ordered the women to return their daughters to the Beit Yaakov girls' school in the West Bank settlement of Immanuel.
Dozens of the families' fathers were jailed for defying the school integration ruling.
The families at the centre of the legal battle come from a strictly observant sect of Hasidic Jews called Slonim, who have Ashkenazi lineage.
They have pulled their children out of the school saying the less observant students would be a bad influence on them.
The parents do not allow influences such as televisions and the internet in their homes.