Soldiers used stun grenades against the rioters, but have not attempted to seize the building.
Reports say some Palestinians have retaliated by throwing stones at the settlers.
The Israeli military says Jewish settlers in other parts in the West Bank have also blocked roads and thrown stones at Palestinian cars.
In the northern West Bank, near Nablus, dozens of settlers clashed with Palestinians and border police in a show of support for the Hebron settlers. There were several arrests.
Several hundred hard-line religious settlers live in the centre of Hebron under heavy military guard amid some 150,000 Palestinians.
The settlers say that they bought the house in question in a legal transaction from its Palestinian owner for nearly $1m (£660,000), but he says he pulled out of the deal.
Israel's supreme court ordered the eviction in November but settlers have refused to leave.
They have been involved in several clashes since the order was issued, and have desecrated a mosque and a Muslim cemetery.
Hebron is holy to both Jews and Muslims as the site of the cave that Abraham bought as a burial site for his wife Sarah.
All settlements in the West Bank, including East Jerusalem, are considered illegal under international law though Israel disputes this.
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