Members of al-Qaida's Syria wing, Al-Nusra Front, who with several militant groups took over the checkpoint Wednesday, said the rebels were "holding ground" despite heavy shelling. The checkpoint lies about 20 km (12 miles) west of the Syrian town Quneitra, which is under state control.
At least six rebels were killed in the fighting, added Abu Iyas al Horani, a spokesman for another of the rebel groups said. The Syrian Observatory for Human Rights said 20 Syrian soldiers and 14 rebel fighters had been killed.
The crossing between the two countries is monitored by the United Nations, with each country operating its own posts about 200 meters apart.
Two Israelis, a soldier and a civilian, were wounded by stray bullets during the fighting. Israel responded with light artillery fire, but it has tried to avoid getting pulled into Syria's three-year civil war.
Rebels had captured the Quneitra border crossing last year, and control many of the villages in the area near northern Israel. Al-Nusra has regained a foothold in southern Syria this year, after losing ground to its rival, the Islamic State.
Below, footage posted by Syrian rebels of the captured border crossing.