The Israeli jets allegedly aimed to attack a military facility and caused an extensive damage, the Syrian Armed Forces said in a statement.
"Israeli warplanes at 2:42 a.m. today fired a number of missiles from Lebanese air space, targeting one of our military positions near Masyaf, which led to material damage and the deaths of two members of the site," the army said.
The statement further warned against the "dangerous repercussions of this aggressive action to the security and stability of the region."
"This aggression comes in a desperate attempt to raise the collapsed morale of the ISIS [Daesh] terrorists after the sweeping victories achieved by the Syrian Arab Army against terrorism at more than one front, and it affirms the direct support provided by the Israeli entity to the ISIS and other terrorist organizations," it added.
The attack was carried out about 60 kilometers east of the city of Tartus, where Russia has a naval base. In March 2016, Putin ordered the pullout of the bulk of the Russian contingent in Syria as the campaign's objectives had broadly been completed. Following Putin's announcement of the withdrawal, Moscow said that some Russian military personnel would remain at the Hmeymim air base as well as the naval facility at Tartus to observe the implementation of the ceasefire in Syria.
Previously, Israeli military planes were also carrying out airstrikes on the Syrian government forces. In February, they hit the Syrian Army positions stationed in the western countryside of Damascus near the Lebanese border.
The Syrian army condemned Israel's move.
In early February, an Israeli helicopter reportedly fired at Syrian government forces' positions in the province of Quneitra in southern Syria, after a shell landed in the Golan Heights.
The Golan Heights, internationally recognized as Syrian territory, was seized by Israel during the Six-Day War in 1967. In 1981, the Israeli parliament voted to annex two-thirds of the region. The United Nations has repeatedly stated that Israel's occupation of the Golan Heights is illegal, calling for it to be returned to Syria.
Since 2011, Syria has been engulfed in a civil war, with government forces fighting against numerous opposition and terrorist groups, including al-Nusra Front and Daesh, banned in a range of countries, including Russia.