The protestors gathered at the corner of Bar-Ilan and Yechezkel Streets in the capital, and also headed towards the entrance to Jerusalem on Highway 1. Some haredim set garbage bins on fire during the protests.
Earlier, hundreds of police officers deployed at the southern hospital ahead of the beginning of work to remove the ancient graves, as part of the construction of a new emergency room at the medical facility .
Forces at the site include mounted police and special riot police. Police officials stressed that they will adopt all means necessary to keep the peace and that commanders were ordered to act as they see fit in order to avert disturbances.
A team of archeologists at the site started to clean the graves after midnight ahead of their removal. Another team was expected to arrive in the morning and start with the actual digging.
Authorities also prepared to stop haredi buses heading for the hospital in order to protest there.
Hundreds of haredim were expected to arrive at Barzilai Saturday night and Sunday morning to protest the relocation of disputed tombs.
'Struggle doomed to failure'
Several buses left Jerusalem's Mea Shearim neighborhood around midnight on Saturday and possibly also departed from other areas around the country where members of the radical Eda Haredit sect live.
The Atra Kadisha organization, which is heading the struggle against the graves' removal, prepared ahead of time for the police's heavy deployment and sent a few yeshiva students ahead earlier to spend the Shabbat at the hospital site.
The organization was concerned that police would close off the area before they begin digging the graves, or that they would embark on the work earlier than planned.
The decision to remove the tombs provoked great anger among various elements in the Eda Haredit sect who strongly objected to the move, arguing that the graves in question belong to Jews.
Vehicles with loud speakers traveled through haredi neighborhoods in Jerusalem Friday and announced that senior rabbis were calling on the public to protest. However, members of the Eda Hardit conceded that their struggle is doomed for failure.
"It's impossible to stop a government decision," one of the struggle's leaders told Ynet. "This entire removal project is an operation that will last 24 to 36 hours, and we're there mostly in order to protest, and less for the purpose of trying to stop it.