In a video of the incident, a man can be seen approaching another man with a knife drawn and attempting to stab him.
Since the death of hilltop youth Ahuvia Sandak last month, Yesh Din investigators say they have received verified reports of 41 different cases of Israeli settlers attacking Palestinian.
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.