The Kalibr cruise missiles launched by the Rostov-on-Don submarine successfully hit the designated targets in Raqqa, Defense Minister Sergei Shoigu reported to President Vladimir Putin.
The submarine was in a submerged position during the launch, he added.
Putin noted that the new cruise missile can be equipped with both conventional and nuclear warheads, adding he hopes that the latter "will never be needed."
Shoigu said Tu-22 bombers also took part in the latest raids, performing 60 combat sorties in the last three days.
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Shoigu said the Russian military had informed Israel and the United States about the airstrikes before launching them.
A US defense official, speaking on condition of anonymity because he wasn't authorised to discuss the matter publicly, confirmed that Russia notified the US in advance.
The US official said at least 10 cruise missiles were launched from Russian surface ships in the Caspian Sea and at least one missile was fired by a Russian submarine in the eastern Mediterranean.
He showed Putin the plane's flight recorder, which he said Syrian and Russian troops had recovered from the crash site.
Putin ordered the flight recorder to be studied in the presence of foreign experts, adding that the data will show the plane's flight path.
Moscow's relations with Ankara have been badly strained over the downing.
Turkey said it shot down the aircraft after it violated Turkey's airspace for 17 seconds despite repeated warnings.
Russian Foreign Ministry spokeswoman Maria Zakharova dismissed Turkey's complaint about a sailor on a Russian navy vessel pictured on its deck with a portable air-defense missile while the ship was cruising across the Bosporus. Turkey denounced the incident as a provocation and summoned the Russian ambassador to protest.