The deal will see the Syrian government restore control over all border posts across the Syria-Jordan border, as the government institutions will return to operation in Daraa, according to SANA.
Meanwhile, in eastern Syria a booby-trapped auto exploded late Friday in the village of al Basira, in the eastern countryside of Deir al Zour, which is controlled by US -backed Kurdish-led Syrian Democratic Forces, or SDF.
The capture of the Naseeb border crossing came hours after the rebels announced they had reached an agreement with Russian mediators to end the violence in Daraa province and surrender the crossing.
He obtained "control over the Syrian-Jordanian border areas in Daraa, the gradual disarmament of the rebels' heavier weapons, and the opportunity to rebuild his government's influence in southern Syria", the analyst at the Washington-based Center for a New American Security said.
The people who left their towns and cities in Daraa will return to their homes, according to the deal.
However, years after the eruption of the Syrian tragedy and the global community's ongoing silence over the displacement of over 5 million Syrians overseas and 10 million inside the country, we do not expect its neighbors to take on more than they have already handled. The details of this passage are expected to be discussed in the coming weeks.
Global monitors said that more than 320,000 people have fled the attacks and have been forced to sleep in open spaces or makeshift shelters near the border.
Syrian opposition activists reported intense shelling and airstrikes on the rebel-held village of Um al-Mayadeen, few kilometers (miles) north of the Naseeb border crossing.
"The solution is political and the protection of civilians, preventing their displacement and saving the (Syrian) brothers more suffering is everyone's responsibility", he wrote.
Assad's next target in the south-west appears to be rebel-held areas of Quneitra province at the frontier with the Israeli-occupied Golan Heights, where fighting between insurgents and the government escalated on Friday.
But Abazeed said the evacuation of opposition fighters and their families planned for Sunday was temporarily put on hold due to "an exchange of fire" between rebels and regime forces.
The onslaught has reportedly forced tens of thousands of civilian residents to flee to areas near Syria's border with Jordan. This would split the territory in two.
The reporter said that the army units started securing Daraa global highway towards Naseeb border by combing the highway's both sides and removing the barriers set up by terrorist groups.
Regarding the injuries of the displaced people, medical sources said that the injuries were caused by shrapnels on the first day of the bombing, but the following days, incoming cases mainly suffered from dehydration and intestinal infections.
Syria's war has killed 350,000 people and displaced millions of others since it started with the brutal repression of anti-Assad protests in 2011.