Hardline protesters on the roof of the Kfar Darom synagogue fought back troops for hours by throwing acid and other substances at them.
They used mirrors to try to dazzle the soldiers and policemen, who avoided using violence against them.
Away from the synagogue, settlers wept as the moment of eviction arrived.
Some chose to walk away on their own, others let the soldiers carry them - and some ran.
Israeli commanders said they hoped people would co-operate during the pullout.
Earlier, settlers threw nails on roads around Kfar Darom to puncture the tyres of vehicles coming to take them away.
Outside the Neve Dekalim settlement, a soldier wept along with his sister, a settler, as security forces lined up to clear the synagogue.
Children who have grown up on the settlements face a new start in Israel.