"At exactly 17:22 (1422 GMT) this afternoon, the Israeli enemy carried out strikes... from the direction of the Mediterranean Sea targeting some of our air defence sites in Tartus," the official news agency SANA quoted the source as saying.
"The aggression led to the death of two soldiers, and wounded six others," it added.
During more than a decade of war in Syria, neighbouring Israel has launched hundreds of air strikes on its territory, primarily targeting Iran-backed forces and Hezbollah fighters as well as Syrian army positions.
The Syrian Observatory for Human Rights war monitor said Wednesday's strikes also targeted a weapons depot belonging to the Iran-backed Hezbollah group.
The British-based monitor with a network of sources inside Syria confirmed the death of the two soldiers, adding that a fighter whose nationality was unknown was also killed "in attacks believed to be Israeli missile fire".
Since the start of the war in Syria, Israel has carried out hundreds of air strikes on Syrian territory, mainly targeting forces backed by Iran and Lebanese Hezbollah, allies of Damascus and sworn enemies of Israel, as well as the Syrian army.
Israel rarely comments on individual strikes it carries out on targets in Syria, but it has repeatedly said it would not allow its archfoe Iran, which supports Damascus, to expand its footprint there.
When questioned by AFP on Wednesday, an Israeli army spokesman said he didn't comment on "foreign media reports".
Later in the evening, Israeli aircraft again targeted Syria, targeting the scientific research centre in the mountains of the village of Taqsis, in the province of Hama, where explosions were heard, the Syrian Observatory said, reporting no casualties.
Syria's war has killed more than half a million people since it broke out in 2011, sparked by the repression of pro-democracy protests.
It quickly escalated into a deadly conflict that pulled in foreign powers and jihadist insurgents.
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