Syria's army accused Israel of hitting one of its positions, killing two people in an attack earlier the same day that a monitor said targeted a site where the regime allegedly produces chemical weapons.
"We are determined to prevent our enemies harming, or even creating an opportunity to harm, the security of Israeli citizens," Avigdor Lieberman said in Hebrew, in remarks broadcast on Israeli television.
"We shall do everything in order not to allow the existence of a Shiite corridor from Tehran to Damascus."
The site struck near Masyaf, between the central city of Hama and a port used by the Russian navy, is reportedly used by forces from Syria's allies Iran and the Lebanese Shiite militia Hezbollah.
Israeli planes have previously carried out strikes believed to have targeted the transfer of weapons to the Iranian-backed Hezbollah, which fought a devastating war with the Jewish state in 2006.
Israel has long warned it would not allow the transfer of sophisticated weaponry to Hezbollah and has accused Iran of building sites to produce "precision-guided missiles" in both Syria and Lebanon.
In comments made earlier, the head of Israeli military intelligence, Major General Herzl Halevi, did not mention Thursday's strike directly but warned his country's enemies "near and far".
"Serious security threats to Israel are presented by armed organisations most of them financed and aided by Iran," he said in a public address.
"We are dealing with these threats, both near and far, with determination and our enemies in every arena know very well the combination of (our) precise intelligence and operational capabilities."
