They captured the Nassib border crossing a day earlier, after the militants announced they had reached an agreement with Russian mediators to end the violence in the southern province of Daraa and surrender the crossing.
State-run Ikhbariya TV showed troops at the crossing Saturday, some flashing victory signs and pumping fists in the air, AP reported.
One officer told the TV that troops have taken up positions along the border with Jordan and are removing illegal crossing points.
The militants seized control of the crossing in 2015, severing a lifeline for Syrian exports and disrupting a trade route between Syria and Jordan, Lebanon and oil-rich Persian Gulf countries.
Taking back the Nassib crossing paves the way for the Syrian president to reopen a trade artery vital to his hopes of reviving the Syrian economy and starting to rebuild government-held areas.
Assad’s next target in the southwest appears to be Quneitra province at the frontier with the Israeli-occupied Golan Heights, where fighting between militants and Syrian forces escalated on Friday.
Government advances in Daraa since mid-June had brought large parts of the province back under state control.