Al-Masdar News reports that one of the targets was a Syrian army ammunition depot in the countryside between the towns of Kiswah and Sahnaya.
An Iranian military base was struck around 12:30 a.m. near the city of Al-Kiswa, about eight miles southwest of the capital, the Syrian Arab News Agency said.
Syrian state television said Syria intercepted at least two Israeli missiles early Saturday that targeted a "military position". The report added that "our defense forces destroyed two enemy targets". The Israeli planes were said to have come from the direction of Lebanon.
The extent of the damage is not yet clear although the TV report spoke of material losses at the base.
A report from the BBC in September alleged that Iran had established a military base in Syria, south of the capital; while Iranian forces may not have an overwhelming presence in the country, numerous militias - including Lebanon's Hezbollah - that are aligned with the Syrian regime are bankrolled and armed by the Islamic Republic. Israel has not confirmed that attack either. However, it comments that the alleged Israeli attack came three weeks after BBC reported that Iran was building a permanent military base in Syria just south of Damascus.
Israel has grown deeply alarmed by Iran's expanding clout during the conflict, and has warned it would act against any threat from its regional foe Tehran.
Iran has provided critical support to President Bashar al-Assad's military in fighting Syrian rebels and Islamic State militants. Iran-backed Shiite militias, including Hezbollah, have helped Damascus regain control of swathes of the country.
Israel seized 1,200 square kilometres (460 square miles) of the Golan Heights from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the worldwide community. The British broadcaster commissioned a series of satellite pictures that showed widespread construction at the site.