The Syrian Observatory for Human Rights said heavy explosions were heard in the area and electricity was cut off throughout Damascus. The "blatant assault" caused material losses at the base, state media reported.
Israel has also struck several Syrian military facilities since the conflict began, mostly near the Israeli-occupied Golan Heights.
The Syrian army has fired at least four surface-to-air missiles at Israeli aircraft as the regime launched an attack against the western countryside of Syria's capital Damascus, reports say.
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 report claimed that some of the missiles had been intercepted by Syrian air defenses.More news: Allardyce wants ex-Liverpool duo in Everton setup
The Israeli entity is closely linked to the terrorist organizations in Syria.
"At half past midnight (local time, Saturday), the Israeli enemy fired several surface-to-surface missiles at a military position in Damascus province", SANA news agency reported. Sky News said the strike had been conducted with air-to-surface missiles from Lebanese airspace.
Israel's Prime Minister Benjamin Netanyahu has recorded a video message for the upcoming Saban Forum in Washington. There has been no official Israeli comment on the attack, however, the message is clear, that Iranian bases will not be tolerated, as senior officials in Israel have stated. Satellite images commissioned by the BBC show construction activity at the site from January to October, 2017.