Three Syrian tanks entered the demilitarized zone on the Golan Heights on Saturday afternoon.
The IDF was waiting for the United Nations' Disengagement Force on the Golan Heights to oversee the withdrawal of the tanks.
The tanks, which were involved in heavy clashes with Syrian rebels, encroached the decades-old ceasefire agreement between Jerusalem and Damascus.
The vehicles entered Beit Ajam, which is close to an IDF position on the border. Earlier on Saturday, local residents near the Syrian border reported hearing heavy exchanges of fire between the Syrian army and rebels.
Israel lodged a complaint with the United Nations over the ceasefire violation. The defense establishment has concluded, however, that the tank movement is linked to the Syrian civil war and not intended as an act of aggression against Israel.
Nevertheless, the IDF raised its alert level in the Golan Heights region.
The Northern Command has been on the lookout for such a development since Syrian infighting approached the Israeli border several months ago. The Northern Command remains committed to a policy of zero-tolerance to challenges to Israeli sovereignty from Syria.
In October, the IDF evacuated tourists from the top of Mount Hermon after sighting dozens of Syrians – many of them armed with guns – in civilian clothing approaching the Israeli border.
The suspects, who may have been rebels, did not infiltrate the border, and stopped their approach to the fence some 500 meters away from the international boundary.
The border with Israel has not been the only frontier affected by Syrian infighting. In October, Turkey's military struck targets inside Syria in response to a mortar bomb fired from Syrian territory which killed five Turkish civilians, while Syrian forces and rebels clashed at several sites close to the Turkish border.
Army intelligence has also provided a gloomy forecast for the border after Assad's downfall, concluding that radical jihadi groups will raid abandoned Syrian army bases, stock up on weapons, and turn their sights to the Israeli border.
The Northern Command has been preparing itself for such a scenario.