In a statement it said Pope Francis shared the "unspeakable pain" suffered by the families of the victims.
The bodies of Naftali Frenkel, Gilad Shaar and Eyal Yifrach were found on Monday evening after they went missing more than two weeks ago.
They were discovered under a pile of rocks near the Palestinian town of Halhul. They were last seen at a junction between Hebron and Jerusalem as they hitchhiked home.
Israel blames Palestinian Islamist group Hamas and has promised those responsible will pay.
Hamas denies any involvement and warned Israel any retaliation over the deaths saying "the gates of hell will open".
Director of the Holy See Press Office, Fr. Federico Lombardi said: ''The murder of innocent people is always an execrable and unacceptable crime and a serious obstacle on the path to that peace for which we must continue to tirelessly work and pray.
"Violence calls more violence and feeds the deadly circle of hatred.
''Pope Francis shares in the pain of the families affected by this murderous violence and the pain of all those affected by the consequences of hatred, and asks God to inspire in all thoughts of compassion and peace."
Paul Calvert is a church volunteer based in Jerusalem.
He told Premier's Antony Bushfield on the News Hour what the reaction has been following the discovery of the teenager's bodies.
When they first disappeared a huge search operation was launched across the West Bank which resulted in the arrest of more than 400 Palestinians and the death of five.
On Tuesday morning Israel bombed dozens of sites in the Gaza strip mostly belonging to Hamas, though the airstrikes were not directly linked to the death of the students.
Israeli Defence Force (IDF) spokesman Lieutenant Colonel Peter Lerner said: "At this time thousands of troops and commanders continue their task.
"For us the mission hasn't finished yet. We will continue to look for those responsible for this murder, those terrorists of Hamas.
"Blockades have been set up where the teenagers were last seen by Israeli security forces which has also closed down entire areas nearby.
The President of the Palestinian Authority, Mahmoud Abbas, has called an emergency meeting of his team and expressed "regret" for the deaths.
Middle East Minister Hugh Robertson responded to an urgent question in the House of Commons describing the deaths as "an appalling act of terror".
He said: "There's no reason, belief or cause that can justify the abduction and killing of innocent civilians.
"We send our deepest condolences to the families of Gilad Shaar, Naftali Frenkel and Eyal Yifrach. The Government remains in close contact with both the Israeli and Palestinian authorities. The urgent priority is to hold those responsible to account under the rule of law and we stand ready to do everything possible to help."