The Israeli army on Sunday said its air defence systems intercepted Syrian missiles over the Golan Heights.
It warned Syrian forces not to attack Israeli territory or forces.
The rocket was shot down by the Israeli military's Iron Dome missile defense system before it breached Israeli airspace, causing no damage. The nature of the attack was unclear on Sunday.
"It is will be hard for Israel to absorb this without a response", he said.
According to Arab media reports, including in Syria, it was in all likelihood a response to an attack against Hezbollah positions.
Nevertheless, daytime strikes by Israel against targets in the war-torn country are extremely rare with the IAF operating during the night.
The military statement did not specify where the rocket had been launched from. "It's permanent", he said. SANA reported that "over eight targets" exploded over the capital, adding that most of the Israeli missiles had been intercepted.
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A week and a half ago, Israel attacked Iranian munitions warehouses in the heart of Damascus.
The UK-based Syrian Observatory for Human Rights said the blast targeted a military intelligence department.
The incident followed Syria's state news agency SANA earlier reporting that Syria's own defence systems had "prevented Israeli air strikes from achieving their objectives in the south". These kinds of flights have been seen as suspicious over the previous year amid allegations that Iran delivers weapons to Syria and Hezbollah using different airlines as cover.
The prime minister said that "in the past 36 hours", the IAF hit Iranian arms depots near Damascus airport. Israel and American defense officials have said these types of ostensibly civilian cargo planes are often used to transport advanced weaponry from Tehran to pro-Iranian militias, fighting in Syria, including the Hezbollah terror group. As a result, it is subject to sanctions by the US Treasury Department.
The Al Quds Al Arabi newspaper reported on Friday that Russian Federation had conveyed to Israel its intent to renovate Damascus International Airport and warned the Israeli government against striking targets, believed to be Iranian arms depots, in the airport's proximity.
Israel has pledged to stop its main enemy Iran from entrenching itself militarily in neighbouring Syria.
With the presence of Iranian and Hezbollah forces, Israel's northern front has become the IDF's number one priority with former IDF Chief of Staff Lt. -Gen.