The Gaza pullout, hailed by Palestinian resistance as a victory and assailed by its Israeli opponents as surrender to violence, will mark the first removal of Jewish settlements from land that Palestinians want for a state.
Military convoys brought troops to the biggest settlement of Neve Dekalim and several expected strongholds of resistance at the start of the evacuation of the 21 Gaza settlements, an operation which the army hopes to complete by 4 September.
By the time the deadline passed at midnight (2100 GMT) on Tuesday, the mood in Neve Dekalim had shifted from anger and despair towards resignation.
Some settlers loaded belongings into containers with the help of soldiers.
Forlorn youths sat on the dusty kerb of the entrance to Neve Dekalim, blankly watching military and police vehicles go in and out.
Some said they planned to make their last stand in the Jewish synagogue.
Palestinians hailed the pullout as
victory for their resistance
"It's truly difficult to live with what's happening but we're still praying for a miracle," said teenager Sarit Noy.
Yael Yarim, 50, who was preparing to leave, said: "My heart has been broken."
Settlers who had said before the deadline expired that they were ready to depart will be allowed to send a family member back to help pack belongings after settlements are evacuated, an army spokesman said.
The army estimated about half of the 8500 Gaza settlers remained in defiance of Prime Minister Ariel Sharon's plan to "disengage" from occupied areas he said have little security value for the Jewish state.
A majority of Israelis back the plan.
Some of Gaza's settlements appeared deserted by midnight, while settlers elsewhere waited for an expected confrontation at dawn with soldiers ready to forcibly evict them from the strip Israel occupied in the 1967 Middle East war.
The Israeli military said three Gaza settlements were empty and most settlers had left three others.
But about 5000 hardcore opponents of the withdrawal have slipped into Gaza settlements in the past few weeks in spite of a partial military closure of the area. Their presence has aroused fears that violence could erupt.
In Kfar Darom, a stronghold of the religious far-right, no settlers said they planned to leave. Shifting huge concrete blocks, they reinforced the synagogue as a possible redoubt.
"I look with hope to the future, that the price we are paying ... will in the end bring about a positive change in Israel's situation"
Israeli defence minister
Unarmed 16-member evacuation squads made up of soldiers, police and paramilitary police have been training for the operation for weeks, practising scenarios that include violent resistance.
One settlement, Dugit in the northern Gaza Strip, is already empty. Residents of two of the four West Bank settlements designated for evacuation have also left.
Officials say 66% of settler families have accepted compensation deals. Those who refused to go could lose a third of the money, ranging from $150,000 to $400,000 per family.
The army had a taste of Jew-versus-Jew confrontation on Tuesday, clashing in Neve Dekalim with hundreds of protesters.
After dark, they returned in greater force to urge settlers to take their last chance to get out under their own steam.
Some Gaza settlers preparing to resist evacuation barricaded themselves in synagogues as Israeli troops poured into defiant settlements.
"It's truly difficult to live with what's happening but we're still praying for a miracle"
Sarit Noy, teenage settler
In Neve Dekalim, the largest Gaza settlement, about 2000 people, most of them youthful "reinforcements" from the West Bank, were holed up in the main synagogue, and a similar number of soldiers and police were already deployed in the settlement to haul the diehards out.
Scores of settlers and their supporters congregated in the synagogues at Neve Dekalim and Kfar Darom on Tuesday, dancing around sacred Torah scrolls in a display of religious fervour.
Earlier on Tuesday, Neve Dekalim settlers pelted army troops and their buses with eggs and stones, trying to disrupt a peaceful departure of other settlers who had packed their belongings into huge container trucks.
Police handcuffed and detained several withdrawal opponents, and seemed to target non-residents who have flowed into Gaza in recent weeks.
Israeli Defence Minister Shaul Mofaz said he expected the evacuation to take about two weeks.
"I look with hope to the future, that the price we are paying ... will in the end bring about a positive change in Israel's situation," he said.