"A short while ago, a mortar shell hit an IDF post in the Golan Heights adjacent to the Israel-Syria border, as part of the internal conflict inside Syria. In response, IDF soldiers fired warning shots towards Syrian areas," the army said in a statement.
Military sources told AFP that the army fired a single Tamuz anti-tank missile, a weapon known for being highly accurate, towards the Syrian outpost from which the mortar round was fired.
"We shot toward them, but deliberately missed," the sources said.
Chief military spokesman Yoav Mordechai said on his Facebook page that Israel had fired a "warning shot" at Syria, and noted Israel's fire into its northern neighbour's territory was the first such incident since the 1973 war.
The Israeli army also filed a complaint through the local UN forces, it said in the statement, warning that "fire emanating from Syria into Israel will not be tolerated and shall be responded to with severity."
Earlier on Sunday, Prime Minister Benjamin Netanyahu said Israel was "closely monitoring what is happening on our border with Syria and there too we are ready for any development."
Sunday's cross-border fire was the latest in a string of incidents in which the fighting in Syria's ongoing bloodshed has spilled across the ceasefire line.
More than 37,000 people have lost their lives since the uprising against Syrian President Bashar Assad's rule erupted in March last year, according to the Syrian Observatory for Human Rights.
On Thursday, three stray mortar rounds from Syria hit the Golan, which Israel seized from Syria in the 1967 Middle East war and annexed in 1981 in a move never recognised by the international community.
And on Monday, an Israeli military vehicle patrolling the buffer zone was hit by gunfire, with the army saying it was caused by "stray bullets" from Syria.
No one was wounded, but the incident prompted an Israeli complaint to the United Nations Security Council in which it described the gunfire as a "grave violation" of a 1974 agreement on security in the buffer zone.
Two days earlier, three Syrian tanks entered Bir Ajam village, five kilometres (three miles) southeast of Quneitra, in the demilitarised zone, sparking another Israeli complaint to the UN.
Since Israel and Syria signed the 1974 disengagement agreement, a 1,200-strong unarmed UN force has patrolled the buffer zone.