Only 150-200 displaced Syrians remained near the Naseeb crossing on Monday, UN official Anders Peterson told Jordanian state news on Sunday.
Jordan has played a leading role behind the scenes in persuading Free Syrian Army rebels, whom it and Western powers have long supported, to reach a deal with Russian Federation that could spare southern Syria more bloodshed and destruction.
According to the UN's refugee agency, UNHCR, 60,000 of the more than 320,000 people who have fled the intense fighting since June 19 have been stationed along the border with Jordan.
Once completed, this effectively ends the rebellion across southern Syria.
He said that while the United Nations and partners are doing what they can to deliver life-saving aid to the people of south-west Syria - both from within the country and across the Jordanian border - the security situation is hindering efforts to reach many people in dire need.
Just north of the Naseeb crossing, government workers began clearing debris and wreckage from the main highway joining Damascus and the Jordanian border on Monday, Syrian state news outlet SANA reported.
Footage posted on social media of women and children pleading with King Abdullah to let them in has generated a wave of sympathy in Jordan with the plight of the newly displaced Syrians.
But the key Nasib border crossing remains in opposition hands.
Fleeing civilians have mostly sought shelter along the frontiers with Israel and Jordan, which is already hosting some 650,000 Syrian refugees.
Hours later, regime forces fully retook the town and also seized control of a security checkpoint on the Jordanian border for the first time in more than three years, the monitoring group said.
Negotiations had stalled Wednesday after Russian Federation "insisted" rebel groups surrender their heavy weapons immediately, joint command spokesperson Ibrahim Jabbawi told AFP.
Osama al-Homsi, 26, told AFP he was hesitant to return to his hometown of Jeeza in southeastern Daraa after the deal.
This is the fourth round of negotiations that failed between rebel groups and Russian military. It added that more Syrians are refusing to go back home out of fears of detention or conscription into the army.
The Syrian Observatory for Human Rights, a UK-based war monitor, said at least 28,000 people had returned in the past day to towns in eastern Daraa covered under the truce deal. The rebels will disarm, but in a series of stages.
Assad aims to recapture Syria's entire southwest including the frontiers with the Israeli-occupied Golan Heights and Jordan.
Assad's Iran-backed allies are also fighting in the campaign, defying Israeli demands they keep out of the border area.
A state television correspondent said the rebels had agreed to hand over heavy and medium weapons in all the towns and cities included in the surrender deal.
More than 350,000 people have been killed and millions displaced since Syria's war started in 2011 with a brutal crackdown on anti-government protests.