Border Police deployed at the Tapuach Junction in the West Bank say the two men were carrying knives, a homemade gun and four pipe bombs, the army said.
Israeli security officials say they believe the pair planned to carry out an attack on Israelis at a nearby hitchhiking post, Israel's Channel One said Saturday night.
Israel has issued a travel advisory for the Sinai Peninsula over concerns of a possible terror attack, officials said.
The National Security Council's Counter-terrorism Bureau called on Israelis in the Sinai to return home Saturday after intelligence reports suggested terrorists were plotting an imminent attack against Israelis visiting there, Yedioth Ahronoth said Sunday.
Families were asked to initiate contact with relatives and inform them of the travel advisory, the newspaper said.