Rebel sources said the deal brokered by Russian Federation would allow civilians to return to their villages and towns with Moscow guaranteeing their protection.
Waves of air strikes pounded rebel-held areas of southern Syria after the failure a day earlier of Russian-brokered talks to end the offensive in Daraa province, which has killed dozens and forced tens of thousands from their homes.
Shortly afterwards, an Al Jazeera reporter on the ground saw a convoy of about 10 army trucks with Russian and Syrian flags entering the strategically important Nassib border crossing, held by the rebels for three years.
But both Israel and Jordan have kept their borders closed, despite mounting calls to let Syrians escape to safety.
He says the military operation to retake southern Syria is the final chapter in the liquidation of the Syrian revolution, and he thinks it is part of a broader agreement between the U.S., Israel and Russian Federation to chase Iran and its militia allies from the southern corner of the country.
Commenting on the negotiations, Jumana Ghunaimat, spokeswoman for the Jordanian government, told Al Jazeera: "The solution in Syria is political, not military".
Civilians and rebels in the south may be easily captured by government forces in the future "without protection or witnesses", he explained.
During Syria's seven-year war, it has conducted scores of air strikes on what it describes as Iranian or Tehran-backed targets.
He said Syrian and Russian jets had pummeled towns across the southwest and villages near the border crossing.
Rebel spokesman Hussein Abazeed told AFP that "the deal was the best we could achieve to save the lives of our fighters".
After four days of reduced bombardment, the intense air strikes had resumed on Wednesday following the collapse of talks between insurgent groups and Russian officers.
Syrian President Bashar al-Assad and his allies are fighting to recapture the southwest, one of the last remaining rebel strongholds in Syria along with a region of the northwest bordering Turkey.
The deal, mediated by Russian Federation, will restore state sovereignty over rebel-held areas in Daraa province following a fierce government offensive.
Rebels then handed some 275 square kilometers of territory near the border to government forces without a fight, said observatory chief Rami Abdel Rahman.
But rebels still hold Deraa's western countryside, the southern half of the divided provincial capital, and the prized Nassib border crossing.
Syria's cash-strapped government hopes to recapture Nassib so that it can reopen trade with Jordan to the south.
The bombing barrage sent an estimated 320,000 civilians fleeing the area in what appeared to be one of the fastest displacements in Syria's seven-year civil war, prompting an global outcry and meetings at the United Nations.
But Russia blocked the council from adopting a statement on the issue.