"The rioters were hurling rocks at Palestinian homes in the neighbourhood of Abu Sneina" just south of the city centre, the army said on Saturday, putting their numbers at 150.
Shlomo Saguy, a police spokesman, said about 400 settlers, most of them young, "clashed with police and soldiers who were preventing them from entering the casbah", the historic Palestinian market district.
Security forces had been deployed to prevent the settlers from sacking Palestinian shops or committing other acts of vandalism, he added.
There have been repeated clashes between settlers and security forces in Hebron in recent days ahead of the entry into force on Monday of eviction orders against nine families living illegally in an enclave in the heart of the city.
Israeli troops are threatening to expel the families - a total of about 50 people - who have taken over some of the stalls and neighbouring buildings of a closed Palestinian wholesale fruit and vegetable market.
Israeli authorities shut the Palestinian market 11 years ago, citing security worries. Settlers took it over in revenge for the killing in March 2001 of a 10-month-old girl by an armed Palestinian, arguing that Jews had the property before the creation of Israel in 1948.
In 2003, Israel's Supreme Court backed an appeal by Palestinian traders and ordered that the Jewish settlers be evicted from the market which should then be reopened - neither of which has yet happened.
Under a 1997 agreement with the Palestinian Authority, Israeli troops withdrew from 80% of the city but remain deployed in
the rest to protect the settler enclaves around the burial site of Abraham - a shrine holy to Jews and Muslims.