The Syrian army responded to missiles launched by Israeli warplanes, the Sana news agency stated.
Israeli jets targeted army bases from Lebanese airspace at around midnight on Sunday, it reported.
Israel’s army has not commented. It periodically attacks what it says are threats to Israeli security in Syria.
These include what it has identified as advanced weaponry destined for the Islamist Lebanese militant group Hezbollah and also Iranian bases in Syria.
Israel says it will not allow it is arch-enemy Iran to entrench itself in Syria, Iran’s key ally.
The facilities strike were linked with Iranian forces, the Syrian Observatory for Human Rights (SOHR), a Britain-based checking group, stated.
In the Homs area, a research center and a military airport where Iranian and also Hezbollah personnel are based were targeted, the Observatory said.
Near Damascus, a base hosting the Iranian Revolutionary Guards Corps (IRGC) along with a research facility in Jamraya was struck.
IRGC and Hezbollah members were injured in the strikes, the Observatory said.
In Sahnaya, south of Damascus, four civilians – including a toddler – were killed as a result of Israeli “aggression”, Syrian state-run broadcaster al-Ikhbariya said.