The revelation came as the government of President Bashar al-Assad met a key deadline in an ambitious plan to eliminate Syria's entire chemical weapons stockpile by mid-2014 and avoid international military action.
The announcement by a global chemical weapons watchdog that the country has completed the destruction of equipment used to produce the deadly agents highlights Assad's willingness to cooperate, and puts more pressure on the divided and outgunned rebels to attend a planned peace conference.
An Obama administration official confirmed the Israeli airstrike overnight, but provided no details. Another security official said the attack occurred late on Wednesday in the Syrian port city of Latakia and that the target was Russian-made SA-125 missiles.
There was no immediate confirmation from Syria.
Since the civil war in Syria began in March 2011, Israel has carefully avoided taking sides, but has struck shipments of missiles inside Syria at least twice this year.
The Syrian military, overstretched by the civil war, has not retaliated, and it was not clear whether the embattled Syrian leader would choose to take action this time. Assad may decide to again let the Israeli attack slide, particularly when his army has the upper hand on the battlefield inside Syria.
Israel has repeatedly declared a series of red lines that could trigger military intervention, including the delivery of "game-changing" weapons to the Syrian-backed Lebanese Hezbollah group.
Israel has never officially confirmed taking action inside Syria to avoid embarrassing Assad and sparking a potential response. But foreign officials say it has done so several times when Israeli intelligence determined that sophisticated missiles were on the move.
In January, an Israeli airstrike in Syria destroyed a shipment of advanced anti-aircraft missiles bound for Hezbollah, according to US officials. And in May, it was said to have acted again, taking out a shipment of Iranian-made Fateh-110 missiles at a Damascus airport.
The Fateh-110s have advanced guidance systems that allow them to travel up to 200 miles per hour with great precision. Their solid-fuel propellant allows them to be launched at short notice, making them hard to detect and neutralise.
Israel has identified several other weapons systems as game changers, including chemical weapons, Russian-made Yakhont missiles that can be fired from land and destroy ships at sea, and Russian SA-17 anti-aircraft missiles. Israel's January airstrike is believed to have destroyed a shipment of SA-17s.
Syrian activists and opposition groups reported strong explosions on Wednesday night that appeared to come from inside an air defence facility in Latakia. They said the cause of the blasts was not known.