According to the reports, Syrian forces fired back at the Israeli forces.
The missile attack was believed to be the latest in a series of Israeli attacks on Syria, where a six-year civil war has devastated much of the country and displaced millions of citizens.
The Syrian Observatory for Human Rights confirmed that "presumably" Israeli missiles had targeted "Syrian regime units and its allies" at a military base close to Kesweh, south of Damascus.
Pro-government forces in Syria managed to intercept two of the missiles, Syrian's state-run SANA news agency reported. Israel has vowed to combat Iranian influence in Syria to defend its own interests in the region.
Israel had no comment on the report, but Prime Minister Binyamin Netanyahu had recorded a statement last week that was presented at the Saban Forum, taking place in Washington this weekend, that Israel "will not allow Iran to base itself in Syria and threaten Israel".
SANA says the missile attack occurred shortly after midnight on Friday and caused material damage.
Some media outlets affiliated with the Assad regime and Lebanese terrorist group Hezbollah initially reported that Israeli warplanes targeted an ammunition bunker belonging to the Syrian Army.
Quoting Arabic language al-Masdar news agency, citing unanimous source, said the Syrian military's anti-aircraft missiles were fired from Mezzeh Airbase in rural Damascus in the early hours of Saturday. We will not allow that regime to entrench itself militarily in Syria as it seeks to do for the express goal of eradicating our state, " Netanyahu said in a televised address that will be aired in full at the Saban Forum in Washington, which is taking place this week.