The missiles were aimed at four Israeli fighter jets that were attacking targets in the coastal province of Latakia late on Monday, the Russian ministry said.
It accused the Israeli army of “intentional provocation” and said Israel did not warn them of its operation in the area until one minute before the strike.
The Israeli government has not commented.

Russian reports said that the IL-20 plane with 15 servicemen aboard lost contact with radar near Khmeimim air base near Latakia.
“Connection has been lost with the crew of a Russian Il-20 plane over the Mediterranean Sea 35 kilometres from the Syrian coast as it was returning to the Hmeimim airbase,” the Russian defence ministry said, adding that communications were lost at the time of the suspected Israeli attack.
“At the same time Russian air control radar systems detected rocket launches from the French frigate Auvergne which was located in that region,” Russia’s TASS news agency quoted the defence ministry as saying, according to Reuters.
An Israeli military spokeswoman, when asked about both the reported Israeli strike and the Russian plane, said: “We don’t comment on foreign reports.”