Tens of thousands of ultra-Orthodox Jews have attended the funeral of an influential rabbi in Jerusalem, bringing parts of the city to a standstill.

The city’s entrance was closed on Sunday to accommodate the funeral procession for Shmuel Auerbach, who died on Saturday at the age of 86.

Auerbach was the leader of a breakaway faction of non-Hasidic ultra-Orthodox Jews of European descent. He headed a wing that rejected registering with the military for the automatic deferrals his followers were granted. When some were jailed, thousands took to the streets on his orders and clashed with the police.

Following the 2012 death of Rabbi Yosef Shalom Elyashiv, Auerbach broke away and posed a more radical alternative to Rabbi Aharon Yehudah Leib Shteinman, who died in December at 104.

The ultra-Orthodox Jews are about 12% of Israel’s 8.7 million citizens.

For decades, the ultra-Orthodox have leveraged their significant political power into maintaining a segregated lifestyle. They run a separate network of schools, have sweeping military draft exemptions and receive taxpayer-funded benefits.

Military service is compulsory for most Israeli Jews, and the exemptions for the ultra-Orthodox has fed widespread resentment against them in what is seen as preferential treatment.

The ultra-Orthodox Jews are about 12% of Israel’s 8.7 million citizens Photograph: Ariel Schalit/AP

Benjamin Netanyahu’s government recently rolled back previous legislation that had aimed to increase conscription – only to be struck down by the supreme court. The court has demanded new legislation within a year.

In the meantime, most ultra-Orthodox men have the option of receiving repeated deferrals, as long as they register with the military.

But Auerbach, a prominent Jerusalem rabbi with about 25,000 followers, rejected even this model.