Observatory chief Rami Abdel Rahman said the missile strike targeted a military base near Kesweh, south of Damascus.
The "blatant assault" inflicted material losses at the site near Damascus, the network said.
The Israeli military declined to comment on the incident when asked by CNN about the Syrian claim.
"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.
SANA, the state news agency, claimed Syrian air defenses shot down two of the Israeli missiles.
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UK-based monitoring group the Syrian Observatory for Human Rights also reported explosions near Damascus, which were said to have been caused by a suspected Israeli attack.
Only last week Defense Minister Avigdor Liberman shunned Netanyahu's fears and stated that, "there is no physical Iranian military presence at the moment in Syria".
The Israeli entity is closely linked to the terrorist organizations in Syria. Reports earlier in November said that foreign reports said that IDF planes had bombed several targets in Syria, striking weapons warehouses in the town of Hasya, near the Syria-Lebanon border. Satellite images commissioned by the BBC show construction activity at the site from January to October, 2017.
Netanyahu has previously warned that Iran was building permanent military installations in Syria, and the head of Iran's Revolutionary Guards Corps Qassem Soleimani has been photographed along with other Iranian troops in the country.