Police stormed the house in the Old City area of the town on Sunday.
Security forces coaxed many of the settlers from the building, while others were dragged kicking and screaming outside.
Supporters of the settlers who had also converged on the scene threw eggs and paint at police and scuffles broke out between the two sides.
The eviction was an early test for the government of Ehud Olmert, the new Israeli prime minister.
At the first cabinet meeting of his new government on Sunday, Olmert said he would not allow illegal West Bank settlement outposts to remain.
"In every case where the law is violated, we will respond without compromise, and we won't reconcile ourselves to illegal facts on the ground," Olmert's office quoted him as saying.
Earlier on Sunday, at least 10 police and settlers were injured after stones, bottles and firebombs were hurled at police outside the house.
A dozen settlers were arrested during the clashes, police said.
Settlers claimed they had legally
rented the property
Thirty to 60 settlers had occupied the home, and they had been joined by about 40 hardline settler supporters.
Aliz Amir, the Israeli police chief in Hebron, told Israeli Army Radio: "This is crossing a red line."
Referring to the use of firebombs,he said:"This is a very grave action by lawbreakers."
The Supreme Court had initially ordered the squatters removed by Friday, but then postponed the eviction because of the Jewish Sabbath on Saturday.
"Palestinians will receive much strength today. There is no justice and no righteousness in this corrupt state," said Tzippora Schlissel, 40, after she left the house.
The settlers moved into the house in April, claiming that they had rented the property from its Palestinian owner.
But police believe the rental documents were forged by settlers and that the three families living in the building are there illegally.
Hebron is a holy city to Jews and Muslims. About 500 Jewish settlers live among 160,000 Palestinians in heavily fortified enclaves protected by the Israeli occupation army.