Another three soldiers were injured and there were material losses, according to the statement.
The ministry announced earlier that missiles launched from the Lake Tiberias area in northern Israel targeted positions around Damascus, but were mostly intercepted by anti-aircraft defenses.
Israel has already carried out seven attacks during the current year against Syrian territory, with the last one also in the vicinity of the capital on April 14th.
The Syrian Government condemned these actions, deplored the silence of the United Nations before them, and ratified the right to defend the integrity and sovereignty of the national territory by all legitimate means.
It also denounced that these attacks are part of the direct support offered to terrorist groups, in particular Daesh or the Islamic State, in order to once again destabilize the already liberated areas.