Settler leaders said the eviction was a criminal act and insisted that their protest was peaceful.
"This is a crime against justice and against Jewish history," said Noam Arnon, a spokesman for the Hebron settlers.
"I am sure we will return. Hebron has a long history and we will return."
Settlers as victims?
Jacky Rowland, Al Jazeera's Jerusalem correspondent, said: "The settlers are defying the authorities and they are keen to portray themselves as the victims.
"Within a matter of weeks, the settlers will probably find a way to reoccupy the houses."
The two settler families that took over the structures said they were once owned by Jews.
About 650 Israelis live illegally in heavily guarded enclaves in Hebron, home to about 180,000 Palestinians, and have long sought to expand the Jewish presence in the biblical city.
Settlers in Hebron are among the most militant in the West Bank, territory Israel has occupied since the 1967 Middle East war.
The Israeli army said on Monday it sentenced several soldiers to one month's imprisonment for refusing to take part in the forced removal of the settlers.
"Of the dozen soldiers - 10 ordinary ranks and two officers - tried for 'refusing to obey orders', several were sentenced to four weeks in military prison," a military spokesman said.
The soldiers, most of them religious, told their commanding officers that they would refuse to join in the operation to evacuate the Hebron market, an army spokesman said.
"A number of soldiers from the Kfir regiment training base protested before their commanders this (Monday) morning over the task they had been given," the army said.
General Gadi Shamni, the head of the central army command, ordered the court martial of "two company commanders and some 10 soldiers, who will be removed from their unit", the army said in another statement.
Zvi Handel, an ultra-nationalist opposition legislator, expressed support for the insubordinate soldiers.
"I am proud that we have soldiers who think before obeying illegal orders and refuse to be part of a political game," he said.