The last to leave were protesters in the West Bank settlements of Sanur and Homesh.
Security forces used bulldozers, cranes and bolt-cutters to evict the hardliners who in the end only put up token resistance.
Israeli army Chief of Staff General Dan Halutz said the lack of violence was partly thanks to mediation by religious leaders.
“There has been less violence than we thought. One of the reasons was because rabbis worked to calm tensions,” he said.
The protestors set alight an Israeli flag to express their anger at Prime Minister Ariel Sharon’s withdrawal plan.
About 8,500 Jewish settlers were removed from Gaza in the six-day operation that ended on Monday.
However, about 450,000 settlers remain in about 120 settlements in the West Bank, including East Jerusalem.
Mr Sharon said he will not surrender the main settlement blocks or halt the building of new settlements as required by the US backed roadmap for peace.
But the pullout has nevertheless raised international hopes of a breakthrough in the stalled Middle East peace process.
It was the first time Israel has withdrawn from Palestinian land captured in the 1967 war.
US President George W Bush has praised Mr Sharon for his courage, while Palestinian leader Mahmoud Abbas called to congratulate him.
Despite divisions within Israel, a new poll shows Mr Sharon’s rating has risen.
The radical Palestinian group Hamas has tried to gain political mileage out of the withdrawal, portraying it as an act of surrender.
“We believe that this unilateral withdrawal is a complete failure for the Israeli enemy, it deserves no concession from our side whatsoever.”