Israeli forces shot and killed four Palestinians and wounded 232, 180 of them from live fire, during protests along the border with Gaza on Friday, Palestinian medical officials said.
Meanwhile, a young Palestinian man has died less than a day after being shot by Israeli military forces during clashes between a group of Palestinian protesters and Israeli forces near the border between the Gaza Strip and the occupied territories.
On Saturday, the IDF conducted air strikes on around 80 targets in the Gaza Strip in response to the recent shelling from the area.
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"After contacts between the Islamic Jihad leadership and the brothers in Egypt it was agreed that a comprehensive ceasefire will begin immediately", spokesperson Daoud Shehab said.
The rocket fire aimed by Iranian-backed Palestinian Islamic Jihad terrorist organization is silent now.
Another IDF spokesman, Lt. Col. Jonathan Conricus, said the rocket strikes were ordered by operatives from the overseas branch of Iran's elite Islamic Revolutionary Guard Corps stationed in Syria and warned Israel may not limit its response to Gaza.
On Sunday, Israel reopened the people and goods border crossings with Gaza and on Wednesday renewed the flow of Qatar-funded fuel to the Palestinian enclave, in an indication of its confidence that Hamas would rein in violence.
Hamas, an Islamist terror group that seized control of the Strip in 2007 and seeks to destroy Israel, has acknowledged that dozens of the dead were its members.
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Shortly after the IDF announcement that it had struck the Hamas headquarters in Gaza, rocket sirens sounded in Israeli communities Sha'ar HaNegev and Sderot.
The Gaza targets included weapons production sites and a factory that makes parts for subterranean tunnels, the army said, adding that the later was near a school.
There was no immediate comment from Hamas. Israel said its forces were attacked with grenades and explosive devices hurled by some of the protesters, some of whom breached the border. According to an Israeli army statement, 16,000 Palestinians gathered along the Gaza border.
Thousands of Palestinian demonstrators have come out for 31 weeks to denounce the blockade of the Gaza Strip and call for the right of return of Palestinian refugees to the homes, from which they and their families were displaced during the establishment of the state of Israel.
Israel has threatened to expand its strikes to Iranian forces in Syria, which could lead to a confrontation with Iranian and Hezbollah fighters.
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Oman's foreign affairs minister Yousuf bin Alawi bin Abdullah said on Saturday the sultanate was offering ideas to help Israel and the Palestinians come together but was not acting as mediator.