But the deal was thrown into doubt almost as soon as it was made, with Palestinian militant groups saying they would not halt their attacks on Israel.
Implementation of Sunday night's plan is due to begin on Monday, but the timetable for the various stages remains vague.
Palestinian officials said the two sides had agreed that Israel would withdraw its forces from Gaza and Bethlehem within 48 hours.
But Israeli officials indicated much a looser schedule to allow the Palestinian agencies the opportunity to calm the situation and quell anti-Israeli violence.
Israeli Foreign Ministry spokesperson Yafa Ben Ari told the BBC: "At the moment we have a high level of warnings of future terror activity and that level of warning must cease."
BBC correspondent James Reynolds in Jerusalem says this deal is very much seen as a first step.
A similar agreement was reached earlier in August but it came to nothing.
Palestinian opposition
The militant Palestinian group Hamas has said it would not support the plan.
"Hamas and the Palestinian people reject any agreement which aims at destroying our resistance and ending the intifada, which is what this agreement is aimed at," a spokesman told the AFP news agency.
And Islamic Jihad, another militant organisation, said it would step up attacks on militant targets.
"The Palestinian people's answer will be to escalate the resistance to foil [Israeli Defence Minister Binyamin] Ben-Eliezer's plan," said Khalid al-Batsh, a Gaza Strip leader for the group.
"We in Islamic Jihad reject this agreement because it will consecrate the Israeli occupation of our land," he told AFP.
The BBC's Barbara Plett says that the leftist Popular Front for the Liberation of Palestine (PFLP) has also rejected the agreement and that strong reservations have been expressed within Palestinian leader Yasser Arafat's Fatah movement.
The armed wing of Fatah, the al-Aqsa Martyrs Brigade, has also warned the Palestinian leadership against endorsing the deal.
'Confidence-building'
The agreement to ease the military clampdown was reached by Mr Ben-Eliezer with Palestinian Interior Minister Abdel Razaq al-Yahya.
Mr Ben-Eliezer said the deal was a "confidence-building measure", essential to future progress.
A senior Palestinian official, Nabil Abu Rudeina, said the withdrawals would "prepare the atmosphere" for more pullbacks.
Mr Ben-Eliezer had first presented his "Gaza first" plan to the Palestinians on 5 August.
Discussions then foundered on Palestinian demands that West Banks towns be included in any proposals for Israeli forces to return to the positions they held before the start of the Palestinian intifada in September 2000.
Israeli forces have been in military control of most of the Palestinian towns in the West Bank for the past two months after a wave of suicide bombings by Palestinian militants.
The talks were held in a Tel Aviv hotel after several days of relative calm.