Rocket sirens had sounded in Israeli settlements in the Jordan Valley in the occupied West Bank and two Reuters witnesses heard an explosion a few minutes later.
The military said in its statement that one of the anti-aircraft missiles had been intercepted. The blast was heard as far away as Jerusalem, dozens of miles away. There were no reports of casualties or damage.
The military said in its statement, "Overnight IAF (Israeli Air Force) aircraft targeted several targets in Syria . Several anti-aircraft missiles were launched from Syria following the mission and IDF (Israel Defence Force) Aerial Defence Systems intercepted one of the missiles ."
Israel has carried out dozens of strikes to prevent weapons smuggling to the Iranian-backed Lebanese group Hezbollah, which is fighting rebels alongside the Syrian army.
Iran, Israel 's arch-enemy, has been Syrian President Bashar al-Assad's staunchest backer and has provided militia fighters to help him. Israel is concerned Hezbollah, with which it fought a war in 2006, is trying to obtain sophisticated weapons it could use against Israel .
Last week Israeli Prime Minister Benjamin Netanyahu met in Moscow with Russian President Vladimir Putin to discuss what he charged were Iran's attempts to establish a permanent military foothold in Syria .