Several masked teens began throwing stones at the force, which was conducting a routine patrol.
A Border Policeman was hit in the head and a Civil Administration member was hit in the back with stones.
The force responded by using crowd dispersal measures, and one of the Civil Administration members fired into the air.
Three settlers were later arrested on suspicion they threw the stones at the force, while another suspect, whose identity remains unknown, was arrested on suspicion of assaulting a police officer.
The injured soldier was evacuated to the Beilinson Hospital at the Rabin Medical Center in Petah Tikva.
“This is a serious incident which resulted in the injury of a Border Police soldier, at a place where our forces shouldn’t feel threatened," the Border Police said.
“We responded quickly and arrested three suspects. We’ll always implement a zero tolerance policy when it comes to those who intend to harm our soldiers and security forces, regardless of their religion or ethnicity,” concluded the statement.