A base that was struck Tuesday night in the Kiswah area, about 12 kilometers south of Damascus housed an Iranian military bunker had allegedly been attacked by Israel before, and was the site of weapons factory or convoy.
According to the Agency, the dead were a husband and wife from the town of Sheikh Miskin in the Syrian province of Dar.
Syrian state-run media said Israel struck a military outpost near the capital Damascus on Tuesday, saying its air defences intercepted and destroyed two of the incoming missiles.
Israel has been accused of carrying out a series of deadly strikes on bases in Syria out of which Iranian forces operate.
Iran plans to deploy "very unsafe weapons" in Syria as part of a campaign to threaten Israel, Israeli Prime Minister Benjamin Netanyahu said.
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Iran has blamed Israel for an April 9 strike that killed seven of its personnel at a Syrian airbase and has vowed revenge.
Iran has pledged to "avenge" the deaths of its agents that were killed in air raids on Syrian bases in recent weeks, although Israel has not taken responsibility for those attacks. The reported attack came an hour after President Donald Trump announced he was withdrawing from the Iran nuclear deal, calling Tehran a main exporter of terrorism in the region.
"I think that all recognize the malice of Iran, and that recognize the right of Israel to defend itself", - said the Israeli Prime Minister.
In its statement, the IDF further said that its defense systems had been deployed "and IDF (Israel Defence Force) troops are on high alert for an attack, and any aggression against Israel will be met with a severe response".
Over the last five weeks, Israel has reportedly carried out at least three rounds of strikes against Iran's military presence in Syria.