Israeli Prime Minister Benjamin Netanyahu vowed tough action as he convened an emergency meeting of his Security Cabinet.
"Hamas is responsible, and Hamas will pay," the Israeli leader said in a statement, adding the teenagers "were kidnapped and murdered in cold blood by human animals." In Washington, President Barack Obama urged restraint.
Eyal Yifrah, 19, Gilad Shaar, 16, and Naftali Fraenkel, a 16-year-old with dual Israeli-American citizenship, disappeared June 12 while hitchhiking home from the Jewish seminaries where they were studying near the West Bank city of Hebron. Despite the dangers, hitchhiking is common among Israelis traveling in and out of Jewish settlements in the West Bank.
Lt. Col. Peter Lerner, a military spokesman, said the bodies were found "under a pile of rocks" near the village of Halhul, just north of Hebron.
Binyamin Proper, who was among the civilian volunteers who found the bodies, told Channel 2 TV that a member of the search party "saw something suspicious on the ground, plants that looked out of place, moved them and moved some rocks and then found the bodies. We realized it was them and we called the army."
Shortly after the abductions, Israel accused Hamas of being responsible and launched a frantic manhunt throughout the West Bank, arresting nearly 400 Hamas militants. Last week, Israel identified two well-known Hamas operatives as the chief suspects. The two men remained on the run late Monday. The search for the teens captured the nation's attention. The Israeli media delivered round-the-clock updates, and the mothers of the three teens became high-profile figures as they campaigned for their sons' return. At one point, the women addressed the U.N. Human Rights Council in Geneva to draw attention to their plight. Israelis held daily prayer vigils, including mass gatherings attended by tens of thousands of people at the Western Wall, the holiest prayer site in Judaism, and in a downtown square in Tel Aviv.
News of their deaths prompted an outpouring of grief among Israelis. Friends and neighbors rushed to the homes of the families in the Israeli towns of Nof Ayalon and Elad, and the West Bank settlement of Talmon, while supporters lit memorial candles and prayed. Large crowds gathered in Tel Aviv's central Rabin Square, and at the West Bank junction where the youths were abducted, singing songs and lighting candles shaped in the names of the youths or the Jewish Star of David.
"All of Israel bows its head today," said President Shimon Peres.
Thousands of Israelis have died in wars and militant attacks over the years, and Israel has grappled with the kidnappings of soldiers by militant groups in the past. But the ages of the victims, and the fact that they were not armed, seemed to strike a raw nerve. With Israeli soldiers ordered not to hitchhike, security officials have long feared that civilians in the West Bank could make easy targets for kidnappers.
Hamas frequently encourages its members to try to kidnap Israelis, believing hostages could be used to win the release of militants detained in Israeli prisons. Tensions had also been high since the shooting deaths in May of two Palestinian teens during a stone-throwing clash with Israeli security forces.
Netanyahu was huddling with his Security Cabinet, a group of senior government ministers, late Monday debating a response. But Israel's options could be limited.
After a two-week crackdown on Hamas in the West Bank, few major targets remain in the West Bank. Hamas had already been weakened by seven years of pressure by Israel and the forces of Palestinian President Mahmoud Abbas, and Israeli troops seemed to find very little during the latest crackdown.
Israel could turn its attention toward the Gaza Strip, where Hamas is the main power. Israel has already been battling a wave of rocket fire from Gaza that erupted in response to its West Bank operation, and it could step up the intensity of its reprisals.
Israel has not publicly provided much evidence proving Hamas involvement, and it is not clear whether the kidnappers received orders from higher-ups or acted on their own. The group praised the kidnappings, but never claimed responsibility.
In Gaza, Hamas spokesman Sami Abu Zuhri warned Israel against any broad offensive. Gaza militants possess thousands of rockets, and would almost certainly unleash heavy barrages at Israel if Israel attacks.
"Netanyahu should know that threats don't scare Hamas, and if he wages a war on Gaza, the gates of hell will open on him," he said.
Netanyahu's spokesman, Mark Regev, said Israel would step up its calls for Abbas to dissolve the unity government he recently formed with the backing of Hamas.
Abbas has condemned the kidnappings, and his forces coordinated closely with Israel during the search for the teens. But he has so far refused Israeli calls to end the unity government, which ended a seven-year rift with Hamas. The Palestinian president called an urgent meeting of the Palestinian leadership on Tuesday to discuss the events, his spokesman Nabil Abu Rdeneh said.
Abdallah Abdallah, an adviser to Abbas, said the Palestinians regretted the loss of life.
"We want peace to be created in this part of the world so no mother or no family will be bereaved for the loss of their beloved ones, Palestinian or Israeli," he said.
Abbas says his new Cabinet is committed to his political program seeking peace with Israel. Hamas is not part of his government, but has lent its backing from the outside.
The unity deal ostensibly ended seven years of Hamas rule in Gaza. But the militant group remains in firm control of the seaside territory.
In Washington, Obama condemned the killings and sent his "deepest and heartfelt condolences" to the families of the youths. "As a father, I cannot imagine the indescribable pain that the parents of these teenage boys are experiencing," he said. He also urged "all parties" to refrain from steps that could further destabilize the situation.
Pope Francis, who in May visited the region, shared in the teens' families "unspeakable pain," said the Vatican spokesman, the Rev. Federico Lombardi. In a statement, Lombardi said the "abominable and unacceptable" crime was a grave obstacle to peace and that Francis was praying that God "inspires all thoughts of compassion and peace."