"I can say they have used very strong violence against the policemen, kicked them, spat on them and hurled stones and other objects towards them."
At least six officers were injured and six demonstrators were arrested, Micky Rosenfeld, a police spokesman, said.
It is forbidden to drive or work on the Sabbath according to ancient religious law, and most public buildings are closed at that time.
The minority Orthodox Jews believe that the religious laws should be adhered to throughout Israel.
Some witnesses said that about 3,000 protesters were involved, although this was not confirmed by police.
Demonstrators initially tried to break past a police cordon and into the car park under the city hall building, Rosenfeld said.
However, the police pushed them back to surrounding streets and the stone throwing and use of water canons ensued.
Rosenfeld said that confrontations occurred in other neighbourhoods in the city, which is sacred to Jews, Christians and Muslims.