Golan Heights on Wednesday, according to an Israeli military spokesman and the Syrian Observatory for Human Rights.
Among the fighters were members of al-Nusra Front, a Syrian rebel group with ties to al Qaeda, according to the Israel Defense Forces.
And while the Islamist forces are no match for Israeli troops in the heavily militarized zone, the takeover represents a new dynamic in a war long feared not only for its deadly effects inside Syria but for threatening to widen into a destabilizing regional conflict, CNN's Ben Wedeman reported Wednesday.
"Essentially, now you have the Nusra Front facing off just a couple of hundred meters from the Israeli army," he said, adding that United Nations peacekeepers are stationed between the two.
An activist in the Golan Heights, Shamil al-Jolani, said the Islamist group Ahrar al-Sham al-Islamiya and other rebel groups, not all of them Islamist, were also involved in the fighting.
Video from the scene showed heavy smoke rising from the Syrian side of the crossing. A journalist working with CNN said that heavy shelling and gunfire erupted earlier from the Syrian side but that the situation had since calmed.
Jolani said some fighters were able to reach the crossing despite bombardment by Syrian warplanes. Because of agreements with Israel, Syrian forces could not bomb the forces at the crossing, he said.
During the fighting, three mortar rounds and some small-arms fire crossed into Israeli-controlled territory, IDF spokesman Lt. Col. Peter Lerner said.
An Israeli military officer was moderately injured, the IDF said on Twitter, and Israeli forces responded by striking two Syrian military positions.
Wednesday's fighting marks at least the second time rebels have attacked the crossing.
In June 2013, rebels and Syrian forces battled for control of Quneitra. The violence prompted Austrian troops to pull out of a United Nations peacekeeping force in the Golan Heights. Israel sent tanks and troops to the border for a time, as well.