Word of the attack heightened tensions in the region as U.N. experts sought to dismantle Syria's large chemical weapons arsenal amid the country's 30-month-old civil war.
The Israelis say they don't want to be dragged into this conflict, but keep inserting themselves in what appears to be their own private war with Hezbollah, the powerful Iranian-backed Lebanese movement that is the key ally of embattled Syrian President Bashar Assad.
During the past year, the Israelis have repeatedly mounted operations against targets in Syria amid a conflict that's been steadily pulling in key players across the explosive region and transforming it into an increasingly complex fight involving proxies of the United States, Iran, Turkey and Saudi Arabia that threatens to widen into a regional conflagration.
The Israelis, along with U.S. Arab allies like Saudi Arabia which oppose Assad, were angry when U.S. President Barack Obama decided in September to back off threats of direct military action against the Damascus regime to pursue a diplomatic resolution and to seek a reconciliation with longtime adversary Iran, Assad's main ally.
Syrian rebel sources said the facility at Snobar Jableh, just south of Latakia, was ripped by explosions around 7 p.m. Wednesday. Other reports spoke of one big explosion.
The area was sealed off by Syrian forces.
The Israeli military made no official comment. But the Israelis were blamed for blasting another base near Latakia July 5 in which some of the 72 supersonic P-800 Yakhont anti-ship cruise missiles delivered from Russia in 2011 were reported destroyed.
Despite Israel's claim it doesn't want to become embroiled in the war in Syria, its northern neighbor, it insists it will take action to prevent the embattled Assad regime from transferring advanced weapons systems to Syria's Lebanese ally, Hezbollah, which has fought Israel since the mid-1980s.
The Israelis have carried out at least four strikes against targets in Syria this year, all of them apparently hitting advanced weapons Assad was supposedly transferring to Hezbollah, or which the Jewish state did not want to see fall into Hezbollah hands.
A May 5 attack reputedly smashed a convoy carrying Iranian-made Fateh-110 surface-to-surface missiles intended for Hezbollah.
The first three attacks were clearly airstrikes. But some reports said the July 5 operation involved at least one missile fired from an Israeli Dolphin-class submarine in the eastern Mediterranean.
If that's correct, it would be the first offensive operation carried out by one of the German-built diesel-electric subs which reportedly are capable of launching nuclear-tipped cruise missiles.
The Syrian DamPress.net website claimed Wednesday's attack involved at least one missile fired from the Mediterranean.
Satellite images obtained by Israel's Channel 2 television network showed the facility that was hit Wednesday contained Russian-built S-125 Neva and SA-3 air-defense missile batteries.
Earlier, Lebanese authorities reported six Israeli warplanes flew through Lebanese air space along the Mediterranean coast north of Beirut shortly before Wednesday's attack on course that would take them to Latakia.
Israeli aircraft violate Lebanese airspace daily and their presence over Lebanon does not prove they were attacking the Latakia base -- although earlier attacks on the alleged Hezbollah convoys were conducted by Israeli F-16 jets that flew through Lebanese airspace.
The Israeli air force has been conducting training exercises for long-range flights in recent days, widely seen as rehearsals for a possible air campaign against Iran's nuclear program.
The Israelis are angry about Obama's efforts to secure a rapprochement with Iran, which Israel's hawkish Prime Minister Binyamin Netanyahu considers an existential threat to the Jewish state.
So there was speculation Israel is merely rattling sabers to demonstrate its displeasure at Obama's actions amid a constant Israeli refrain of "we stand alone."
Israeli President Shimon Peres underscored that position Tuesday with a thinly veiled warning to Israel's regional foes that the air force had some deadly moves up its sleeve.
"Not all of the ... air force's capabilities are open to view," he said during a visit to the Palmachim air base south of Tel Aviv. "Whoever derides us and seeks to harass us should take this into account."