Securing it will be a big victory for the Syrian army both symbolically and militarily as the rebels have used the Jordanian border to bring in arms and fighters throughout the war.
The Russia-backed regime offensive has displaced around 320,000 people since June 19, the United Nations says, including tens of thousands who fled south to the sealed border with Jordan.
Russian-backed Syrian forces had launched an offensive in southern Syria two weeks ago.
State-run news agency SANA said the army deployed at the crossing after combing and clearing it of the remnants of "terrorist groups".
Rebels who did not wish to come back under President Bashar al-Assad's rule would leave for the insurgent stronghold in north-west Syria, they said.
Concrete blocks near the Nassib border crossing were plastered with emblems of insurgent factions, while an army checkpoint at the entrance carried photos of Assad.
Syrian regime forces are seen in Nassib border crossing with Jordan in Deraa on Friday.
Last week, rebel forces from Busra a-Sham-notably Shabab a-Sunnah, led by commander Ahmad al-Awdeh-were among the first to formally agree to a reconciliation deal with the government.
It was too early to tell what sort of impact the truce might have, she said, but there was urgent need to get water and shelter for the displaced.
The Syrian Observatory for Human Rights, a UK-based war monitor, said Syrian and Russian air strikes pounded the town and its environs, killing three people.
One of the arches that vehicles crossing the border used to pass under has partially collapsed, with its concrete blocks and metal bars jutting into the air.
Rebel officials say the main differences include whether the rebels surrender their weapons in one go or in phases, before handing over their areas to state control under Russian military police supervision. "The Russian and the Syrian regime offer no safety", he said.
Mr Assad is also aiming to recover control of rebel-held areas of Quneitra province at the frontier with the Israeli-occupied Golan Heights.
However, Mr Assad set his sights on retaking them after defeating rebels in the Eastern Ghouta region outside the capital Damascus in April.
For the anti-Assad rebels, losing the southwest will reduce their territory to a region of the northwest bordering Turkey and a patch of desert in the east where US forces are stationed near the border with Iraq and Jordan.
The de-escalation zone in the southwest was agreed by Russia, Jordan and the USA in June 2017.
"There are large numbers of women and children among the displaced, as well as elderly, injured and sick people and I am especially concerned about them", he continued, adding that among the displaced are local humanitarian workers who have "selflessly served the civilian population throughout the duration of the conflict".
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