The attack took place after Prime Minister Benjamin Netanyahu's security cabinet approved it in a secret meeting on Thursday night, the security source said.
CNN quoted unnamed U.S. officials as saying Israel most likely conducted the strike "in the Thursday-Friday time frame" and its jets did not enter Syrian air space.
The Israeli air force has so-called "standoff" bombs that coast dozens of kilometers (miles) across ground to their targets once fired. That could, in theory, allow Israel to attack Syria from its own turf or from neighboring Lebanon.
Lebanese authorities reported unusual intensive Israeli air force activity over their territory on Thursday and Friday.
A Lebanese security source said his initial impression was that Israeli overflights were monitoring potential arms shipments between Syria and Lebanon, potentially to Hezbollah, a militant Shi'ite Muslim ally of Iran and Assad.
"We believe that it is linked to Israel's concerns over the transfer of weapons, particularly chemical weapons, from Syria to its allies Lebanon," said the official, who asked not to be named.
Syrian opposition sources, usually quick to announce rumors of Israeli air strikes, said they had not heard of an attack on Syrian territory.
Syrian government sources also denied having information of a strike. Bashar Ja'afari, the Syrian ambassador to the United Nations, told Reuters: "I'm not aware of any attack right now."
In January this year, Israel bombed a convoy in Syria, apparently hitting weapons destined for Hezbollah, according to diplomats, Syrian rebels and security sources in the region.
Israel has not formally confirmed carrying out that strike.
Hezbollah fought a 34-day war with Israel in 2006.
Israeli remains technically at war with neighboring Syria. It captured Syria's Golan Heights in the 1967 Middle East war, built settlements and annexed the land. Yet belligerence was rare and the borderland has remained largely quiet for decades.
But Israeli concerns have risen since Islamist fighters linked to al-Qaeda assumed a prominent role in the armed insurrection against Assad. Israelis believe one in 10 of the rebels is a jihadi who might turn his gun on them once Assad is gone. They also worry that Hezbollah guerrillas allied to Assad could obtain his chemical arsenal and other advanced weaponry.
Giora Eiland, a former Israeli army general and national security adviser, said the apparent deadlock in Syria's civil war, now in its third year, meant the Netanyahu government had to be prudent in any military intervention.
"I don't anticipate far-reaching consequences in Lebanon or Syria (from Israel's actions)," Eiland told Israel Radio. "Israel appears to be conducting itself judiciously."
Israeli warplanes have carried out an air strike on a target in Syria, asecurity source in the region said on Saturday, confirming a disclosure by a U.S. official.
The target of Friday's raid was not a Syrian chemical weapons facility, the source told Reuters on condition of anonymity. Israeli officials have declined all comment on the event, which was reported by American media on Friday.
The Jewish state had previously made clear it was poised to resort to force to prevent advanced Syrian weapons, including President Bashar al-Assad's reputed chemical arsenal, reaching Islamist rebels fighting to topple him or his Hezbollah guerrilla allies in Lebanon.
A U.S. official, who also declined to be identified, told Reuters on Friday the air strike apparently targeted a building.