Border Police are still looking for more suspects.
The two men were picked up because they were near the cave at the time of the theft. According to the Border Police, they were also seen on a security video of the site.
Friday’s incident follows one that occurred two weeks ago in which three mezuzot were stolen.
Last Friday, a book of psalms left at the site was ripped up, according to Hebron Jewish community spokesman David Wilder.
Palestinians have access to the site every Friday during Ramadan in order to facilitate prayer at Ibrahimi Mosque, which is located in the same structure.
Palestinians were scheduled to have access to the site three more times this week as Ramadan ends, including Sunday night.
The Hebron Jewish community and MK Orit Struck (Bayit Yehudi) have asked the IDF not to allow the Palestinians access to the site this week.
According to Wilder, the army has approved a ban of Palestinians between the ages of 17 and 32 from entering the mosque on Sunday night. He added that the IDF was weighing additional measures.
The IDF could not confirm Wilder’s statement by press time.