The angry settlers' target was the commander of Binyamin's brigade base, whom they call "traitor", reports Israeli media.
The commander was part of the force that on Friday stopped settlers from entering a military area near the Palestinian village of Kafr Malik. Six Israeli civilians were arrested during the clash.
Earlier in the week, it is reported that over 100 settlers entered Kfar Malik, where they set properties on fire and opened fire on Palestinians who tried to stop them. Three Palestinians are said to have been killed in the unrest.
The vandalism at the military base, whose area of responsibility includes Ramallah, took place during the night until Monday. No one is said to have been seriously injured in the turmoil.