Syria is trying to hurt Israel by arming Hezbollah in Lebanon. Whether or not the orders were issued in Tehran is irrelevant. So Israel feels free to engage in this focused struggle against Syrian-backed Hezbollah.
Syria protests and issues threats about "next time." Israel reminds Syria that Israeli action could be much worse:
Israel sought to persuade Syrian President Bashar al-Assad on Monday that recent air strikes around Damascus did not aim to weaken him in the face of a two-year rebellion, and played down the prospects of an escalation. ...
Intelligence sources said Israel attacked Iranian-supplied missiles stored near the Syrian capital on Friday and Sunday as they awaited transport to Assad's Lebanese guerrilla ally Hezbollah.
Israel has repeatedly warned it will not let high-tech weaponry get to Iranian-backed Hezbollah, with which it fought an inconclusive war in 2006.
Damascus accused Israel of belligerence meant to support outgunned anti-Assad rebels. The air strikes were tantamount to a "declaration of war", it said, and threatened unspecified retaliation.
Assad is having enough trouble with the war he has. He'd be a fool to draw Israel into the fight when Israel limits its actions to the Israeli-Hezbollah fight.