A little before midnight (2100 GMT) on Monday, "the Israeli enemy carried out air strikes on some of our armed forces' positions near the city of Deir Ezzor," leaving "two soldiers wounded," a ministry statement said.
During more than a decade of conflict in Syria, neighbouring Israel has launched hundreds of air strikes on its territory, targeting Iran-backed forces and Hezbollah fighters as well as Syrian army positions.
On September 21, Israeli tanks shelled "two temporary structures" that the Israeli army said were being used by Syrian troops in violation of the 1974 disengagement agreement between the two countries.
Israel rarely comments on individual strikes it carries out on targets in Syria, but it has said repeatedly that it will not allow its arch foe Iran to expand its presence.
Militias linked to Iran's Revolutionary Guards have a heavy presence across Syria, especially around the border with Iraq, and south of the Euphrates in Deir Ezzor province.
The conflict has killed more than half a million people since it broke out in 2011, following the bloody repression of pro-democracy protests.
It quickly escalated into a broader conflict that pulled in jihadists and foreign powers.
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