The officer was lightly injured and treated on the scene, not requiring further medical attention.
The IDF said the video was taken at the end of the incident and showed only a fraction of the events that had unfolded.
Settlers also slashed Border Police vehicles tires, the spokesperson added.
The two structures in Area B were in the Kumi Uri outpost near the Yitzhar settlement.
A security official warned that all illegal actions would be responded to with firm action.
One resident was arrested in the clashes
The group rioted on police bus, broke windows and tried to escape after fearing they were being taken to a Shin Bet detention center.
Forces from both Border Control and the IDF scanned the area shortly afterwards in search of the culprits.
The High Court of Justice ordered the razing because the homes were illegal and built on West Bank land under auspices of the Palestinian Authority.