Their bodies were found in a pit in a field near the village of Halhul.
The families of Naftali Frenkel and Gilad Shaar, both 16, and Eyal Yifrach, 19, have been informed and the bodies positively identified.
All three were last seen at a junction in Gush Etzion, south of Jerusalem, on June 12.
Israel has accused two West Bank Palestinian men who are affiliated with Hamas of abducting the teenagers.
Amer Abu Aysha and Marwan Kawasme have been missing since the June 12 kidnapping.
An emergency cabinet meeting is currently in session and the Israeli military has set up blockades around the immediate area.