Syrian Air Defenses intercepted and downed most of the missiles, with damage limited to the depot, the agency reported.
The strikes came after rockets were fired at Israeli military positions in the occupied Golan Heights overnight.
Syrian Air Defenses intercepted and downed "a number of hostile targets" over the western countryside of Damascus on Tuesday, according to the Syrian state-run news agency SANA.
"It's an Israeli raid", said Rami Abdel Rahman, who heads the war monitor.
Lebanon has confirmed Israeli warplanes violated its airspace.
"An aerial defense system was activated against an anti-aircraft missile launched from Syria", a military spokesperson said in a statement reported by The Associated Press.
News reports tied between the strike and the earlier arrival of an Iranian cargo jet in Damascus.
During the more than seven-year conflict in neighbouring Syria, Israel has grown deeply alarmed by the expanding clout of Iran - a key ally of Syrian President Bashar al-Assad.
The Hezbollah leaders were on their way to a conference in Iran, according to Newsweek.
There was no confirmation from the Israeli military of an attack on Syria.
Russian Federation announced it had delivered the S-300 air defence system to Syria in October.
The S-300 systems were delivered to Syria last month, but they are not yet believed to be in use, as the Syrian air defense teams still need to be trained to operate them.
"A number of missiles hit arms depots for Hezbollah or Iranian forces", the observatory said, adding that no casualties or losses were reported.