About 1,000 settlers tried to stop army bulldozers from tearing down structures, some throwing rocks at police and lying on the ground.
The operation to remove the outpost, west of the Palestinian town of Nablus, sparked a row in the Israeli Government, with right-wing members of parliament calling for Israeli Defence Minister Binyamin Ben-Eliezer's resignation.
On Sunday the government also announced its forces would begin a partial withdrawal from the town of Hebron in the West Bank, one of seven Palestinian towns and cities re-occupied by the army in June.
However, army units are to remain in two Palestinian districts overlooking Jewish settler enclaves in Hebron.
The withdrawal plan is modelled on a successful pullout from Bethlehem in August where Palestinian police took over responsibility for security from the Israel army.
Condemnation
Mr Ben-Eliezer has accused the settlers of insurrection and said their action posed a "life-or-death danger".
Israeli Prime Minister Ariel Sharon, usually a champion of the settlement drive, also criticised the settlers' action.
"Israel is a law-abiding nation and any attack on its army, police or security forces is an attack on the government and should be strongly condemned," he said.
Mr Ben-Eliezer ordered the removal of Havat Gilad earlier this week as part of the government's decision to dismantle about 20 unauthorised settlements in the West Bank.
West Bank police spokesman Rafi Yafeh said police and soldiers were outnumbered by the settlers who had gathered to defend the outpost.
Violent clashes broke out and about 30 police and civilians were hurt in scuffles as police dragged about 400 settlers off the site.
Israeli media said hundreds of settlers were still trying to stop police from removing the remaining structures at Havat Gilad on Sunday morning.
"The revolt of the settlers against the government is a life-and-death danger. There are two or three outposts left in this series of evacuations. I intend to carry this out to the end," Mr Ben-Eliezer told Israel radio.
Latest reports on Israeli army radio said the security forces have now begun to dismantle the second part of the Havat Gilad outpost.
Call to quit
The operation to remove Havat Gilad sparked a furious row within the government after troops were sent to the site on the Jewish Sabbath, in breach of religious law.
National Infrastructure Minister Effie Eitam accused Mr Ben-Eliezer of stupidity and cowardice and called for his resignation.
"A figure like this, who is prompted by political panic to make decisions like this, cannot be defence minister in Israel," the Israeli newspaper Ha'aretz quoted him as saying.
Unlike other rogue outposts which usually consist of generators and empty caravans, several families were living at Havat Gilad.
It was named after settler Gilad Zar, who was killed by Palestinian gunmen in May, 2001.