"The burning and desecration of Joseph’s Tomb last night is a blatant violation and contradiction of the basic value of freedom of worship," Lt. Col. Peter Lerner said in a statement.
There were no reported injuries and the fire was swiftly brought under control and extinguished.
The IDF spokesman added that the site would be restored to its previous condition and the government would ensure that freedom of worship returns to Joseph’s Tomb.
The IDF is working to bring the perpetrators of the act to justice, Larner said.
This case of arson follows a recent escalation of the long-standing Palestinian-Israeli conflict, which has claimed the lives of eight Israelis and over 30 Palestinians in the past month.
The core of the Palestinian-Israeli conflict is essentially a struggle over land. Palestinians are seeking the diplomatic recognition of their independent state on the territories of West Bank, including East Jerusalem, and the Gaza Strip.