Military officials characterized the incident as "unprecedented," Haaretz reported Wednesday.
It was the first time extremists carried out an act of vandalism against Israeli military equipment.
Officials said the incident was a "price tag" operation against the army just two days after the military demolished three homes at the Migron settlement near the Palestinian city of Ramallah.
Graffiti sprayed on the vehicles said "Price Tag" and "Greetings from Migron," The Jerusalem Post reported.
Army Radio said the incident was probably carried out by a group.
In addition, they may have received help from a soldier to gain entrance to the base.
An investigation of the incident is under way.