‘A projectile fired from Syria was intercepted by the Iron Dome aerial defence system. No injuries have been reported,’ a military statement said on Saturday afternoon.
‘This is the first time that fire from Syria has been intercepted by the Iron Dome aerial defence system,’ a military spokesman told AFP in response to a query.
Later in the day the army said Iron Dome took down a second projectile.
It was a marked departure from recent tit-for-tat artillery fire and occasional retaliatory air strikes.
Israel deployed batteries on its northern flank as a precautionary measure after a 2015 Israeli air strike against the Lebanese Shia Hezbollah group's forces in Syria.
Israeli public radio said that the military believed the latest fire from Syria was an unintentional spillover from the country's complex civil war which is now in its sixth year.
Israel has sought to avoid being drawn in to the conflict, but has attacked Syrian military targets when fire fell on its side of the divide.
On Tuesday, Israeli aircraft targeted Syrian army positions after what the military said was probably stray fire hit the Israeli-occupied zone.
Syria said it had shot down an Israeli warplane and a drone, a claim denied by Israel.
The increased tension comes after a fragile new Syrian ceasefire brokered by Russia and the United States came into force on Monday.
The truce does not apply to areas held by jihadists such as the Islamic State group.
The Israeli army holds the Syrian government accountable for any fire from its territory, regardless of the source.
Israel seized 1,200 square kilometres (460 square miles) of the Golan from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.
During the 2014 war between Israel and Hamas and other Palestinian militant groups in the Gaza Strip enclave, Israel deployed its Iron Dome system on land to shoot down rockets fired into the Jewish state.
Funding for the missile system was part of an unprecedented $38 billion US military aid package signed in Washington on Wednesday.
The deal covers the period from 2019 to 2028, and will see Israel receive $3.3 billion per year in foreign military financing -- up from $3.1 billion per year currently -- and $500,000 a year in funding for missile defence.