Authorities reported at least 32 police officers have been injured during the planned evacuation which lasted two days.
Israeli police remove settlers and rightist protesters from the last home in the illegal Amona settlement.
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Officers were wearing protective goggles after bleach was thrown at them.
Authorities reported at least 32 police officers have been injured during the planned evacuation.
With the final home cleared, police moved towards the synagogue where some 200 protesters had barricaded themselves inside.
After forcing their way in, officers removed the activists one-by-one.
Built on private Palestinian land, the eviction of Amona was ordered by the Supreme Court after a lengthy legal battle. Most countries consider all Israeli settlements illegal, Israel disagrees.
On Wednesday Israel announced it would establish a new settlement in the occupied West Bank, to help rehouse the settlers evicted from Amona.