The deal will take place in phases across Deraa, but there is no timeline yet, a rebel official 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.
Dozens of Syrian soldiers, as well as Russian military police and armoured vehicles with the Russian flag, patrolled the crossing during a media tour. Plumes of smoke rose from territory to the east and a few explosions rang out in the background.
Reuters Television footage showed a long convoy of tanks and vehicles, carrying hundreds of forces and Syrian state flags, that appeared to be heading for western Deraa province, where insurgents still hold several towns.
Syrian state news agency SANA said troops had taken up their positions on Saturday after conducting clearing operations.
In a live broadcast from the border, state television showed groups of soldiers flashing victory signs, cheering for Assad, and tearing up insurgent flags.
A field commander told Reuters the army had cut off rebel supply routes by seizing two towns that overlook the highway leading to the Jordanian border. "There was fierce and intense resistance," he said.
Only about five towns in southeast Deraa remain in insurgent hands, he added. "I believe they will decide to return to the state's embrace, and if they are late in doing so, then we are ready to end it militarily."
Taking back the crossing paves the way for Damascus to reopen a route vital to its hopes of reviving Syria's shattered economy and rebuilding in territory under its control.
Over the last two weeks, fighting in the south uprooted more than 320,000 people, the United Nations says, in the biggest exodus of the seven-year war. Nearly 60,000 people have gathered near the Jordan border and thousands more are seeking shelter at the frontier with the Israeli-occupied Golan Heights. Both Israel and Jordan, which beefed up their border controls, said they would not let refugees in but distributed aid inside Syria.
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 Deraa covered under the truce deal.
The Syrian Arab Red Crescent (SARC) said a convoy of food parcels and flour bags, from the U.N.'s World Food Programme, headed to Ibta town which came under army control last week.
The military's next target in the southern offensive appears to be the parts of nearby Quneitra province in rebel hands at the Golan frontier.
(Reporting by Firas Makdesi and Ellen Francis in Beirut Writing by Ellen Francis Editing by Helen Popper) ((Ellen.Francis@thomsonreuters.com))