Syrian state news agency SANA said the attack was foiled and did not admit to any losses.
"Air defense intercepts hostile targets over al-Kiswah and downed them", Syrian state media quoted a military source as saying.
Earlier in the day, the Al Hadath TV reported that Israeli air forces had attacked Iranian military facilities near Damascus.
The Israeli military refused to comment on the raid, but denied a report in Russian media that an Israeli plane had been shot down.
Syrian air defenses responded to the attack aimed at the town of Kiswah, south of the capital Damascus Thursday night, destroying at least five missiles.
"At this point, it remains unclear if the launch indeed landed in Israeli territory", it said, adding that Israeli troops were searching the area for possible remnants of the missile.
Israeli jets bombed several areas in southern Syria and near Damascus on Thursday drawing retaliatory fire from the ground, a monitoring group said.. More news: New North American Trade Pact Signed
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Two missiles hit "weapons depots belonging to the Lebanese Hezbollah (militant group) as well as Iranian forces" in Kisweh.
"Furthermore, the report about a strike on an Israeli aircraft or an Israeli aerial target are bogus", said the statement.
Opposition sources say Hezbollah now plays a commanding role in the Quneitra province that neighbors Israel, where it is believed to be training allied militias and hundreds of former rebels.
Israel claims that Iran's presence in Syria as part of an advisory mission requested by Damascus poses a threat to the regime's security.
After the September attack, during which 15 Russian servicemen were killed, Russia and the Syrian government blamed Israel for the crash, and Moscow was quick to equip Damascus with the advanced S-300 air defence system. Operation of the system could thus make Israeli jets far more vulnerable in any future missions in Syria.
Israeli Prime Minister Benjamin Netanyahu had told Moscow his government would continue to hit hostile targets in Syria to prevent Iran from establishing a military presence across the border.