Maj. Nehemia Berki spoke on Monday at a United Nations ceremony marking the reopening.
The Quneitra area was retaken from rebels by the Syrian army its allies in July.
Syrian government forces captured the Naseeb-Jaber border crossing on July 7, following a surrender by rebels.
The Naseeb crossing on Monday. Since then, some Lebanese exporters have relied on sea and air transport for such exports.
The SDF, backed by the coalition, has ousted IS from swathes of northern and eastern Syria, including Raqa, the de facto capital of the jihadists' so-called caliphate.
Economic observers said the border passage generated almost $600 million in trade yearly before war in Syria began in 2011.
A Russia-Turkey deal for Idlib was reached last month, setting up a demilitarized zone and a cease-fire in the province, which is home to 3 million people. The Kurdish-led forces, backed by US -led coalition air power, continue to battle IS militants in Hajin, a small pocket east of the river.
Government forces, aided by Russian air craft and allied militia, chased IS fighters out of the city and most of the western banks of the Euphrates river past year.
The Syrian government began repairing its side of the border crossing in mid-September, Syrian state news agency SANA reported at the time. Last month, the Russian military reported that U.S. strikes using white phosphorus had resulted in major fires and civilian casualties in the eastern Syrian province of Deir Ez-Zor.
Al-Moallem said "real victory" will come when Syria recaptures its territory in full, citing areas in the north including Idlib province, still outside government control. But IS has lost most of its self-declared caliphate in Syria and Iraq over the last two years. He says Syria must find its way back to the Arab fold.
Al-Jaafari added that "no one should isolate Syria" and that he has been advocating dialogue to restore ties.More news: Hamas denies firing rockets, 'regrets' cancellation of Egypt intel visit
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It is known that in the battle killed several terrorists.
Pockets of ISIS fighters were also driven from the region.
The Syrian flag has also been hoisted on the crossing amid the presence of Syrian police and local delegations from Quneitra. It's the fifth group of refugees to return home from Lebanon.
Syria's war has killed an estimated 450,000 people and drawn in regional and worldwide powers, leaving entire towns and neighbourhoods in ruins.
The sources stressed that "the only contact existing with the Syrian side is on the return of displaced persons and is taking place with the Russian side". Last week, President Bashar Assad granted general amnesty to army deserters, a move created to boost the number of returning refugees.
"In the future, if everything goes well, (the Quneitra crossing) will be opened for the transit of people for family visits and for trade", the officer said.
The crossing was once used by the Golan Height's 22,000 Druze to export apples to Syria.
In Quneitra, the UN Disengagement Observer Force, which monitors a ceasefire line separating Israeli-occupied parts of the Golan Heights from Syria, resumed its patrols in the area in August. But the observers left the crossing as Syria's civil war made it unsafe. Security personnel and dogs searched the vehicles.
Previously two of of the most important trade routes for the government, their opening is a victory for the Syrian government which, backed by Russian Federation, has recaptured large swaths of territory from rebels after seven years of civil war.
The Jaber-Nasib crossing between Jordan and Syria reopened first thing Monday morning, with the Quneitra crossing in Israel's Golan Heights following shortly after.
Monday's reopening-though seemingly limited for now-could reflect thawing relations between Amman and Damascus after years of tensions throughout Syria's seven-year conflict, said Sam Heller, senior analyst with the International Crisis Group.