The attempt by Iran to increase attacks, weapons smuggling and incidents in the West Bank is an emerging threat for Israel.
The man was one of a group of masked suspects at the Ma'ale Levona intersection off Highway 60 in the northern West Bank.
Israel's Air Force followed its route and used the Iron Dome to intercept the drone, which was reportedly not a threat to Israeli citizens at any point.
Israel is under pressure from the US to halt settlement activity and to provide the Palestinian Authority with economic gestures.
"We are coming to protest the injustice that has been done and demand Yehiel's immediate release," right-wing protest organizers said.
Footage from the scene shared by Border Police shows Palestinian men, some masked, hurling rocks inside the tomb complex as well as at oncoming traffic.
Washington, whose traditionally close ties with Israel have become strained, has described the incident as a "terror attack by Israeli extremist settlers."
Yered was released to house arrest on Wednesday night, but only after police had appealed such an order five separate times in three courts.
Elisha Yered along with another settler was arrested on Saturday morning for their involvement in the clashes in Burka.
The State Department Near Eastern Affairs account on Twitter sent two statements within seconds about the weekend’s violence.
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