At midnight on Sunday (0700 AEST Monday) troops closed Kissufim border crossing and formally outlawed the presence of settlers in the territory after a 38-year occupation.
Eviction notices to the 9,000 settlers in all 21 settlements in Gaza, and four of 120 in the West Bank, also went into effect at midnight.
As the operation began, furious settlers smashed car windows and set fire to tyres at the entrance to the Neve Dekalim settlement in southern Gaza.
Efforts by officials from the settlers’ lobby Yesha to calm the crowds fell on deaf ears and journalists were assaulted by irate youths.
“This is not what we planned but we cannot control these young people,” one Yesha leader, Shaul Goldstein, said.
“This activity undermines our struggle.”
Israeli troops plan to knock on the doors of the Gaza settlers’ homes later on Monday and tell them they have 48 hours to leave.
The army will begin forcibly evacuating residents from Wednesday, before bulldozers destroy their homes.
Hundreds of Gaza settlers have signed compensation deals to leave the territory before the August 17 deadline, but the army said about 5,000 opponents of the pullout managed to reach the enclaves.
Under the slogan “Jews don’t expel Jews”, settlers have waged an emotional campaign against Prime Minister Ariel Sharon’s disengagement plan.
Mr Sharon has justified his project by arguing that it will enable Israel to retain control of West Bank settlement blocs where the vast majority of the 245,000 settler population lives.
About 7,500 Palestinian security personnel are patrolling the settlements perimetres to prevent any attacks by militant groups such as Hamas, which has portrayed the pullout as an act of Israeli surrender.
Meanwhile the United Nations said it will pull out its non-essential foreign staff from Gaza after a spate of kidnappings.
A sound technician from France 3 television, who was taken by three gunmen from his hotel in Gaza City, was the latest to be abducted by suspected Palestinian militants.
The abduction is an embarrassment for the Palestinian Authority and comes three days after Palestinian leader Mahmoud Abbas ordered security services to protect foreign workers.