The strike - the first of its kind since November - targeted militants and heavy weapons near the city of Palmyra, the Russian defence ministry said.
The militants had been redeployed from the IS stronghold of Raqqa, it added.
Russia has been carrying out air and missile strikes in support Syrian President Bashar al-Assad since 2015.
Government forces recaptured Palmyra and its Unesco World Heritage-listed ruins with Russian help in March 2016, but were driven out by IS eight months later.
They eventually regained the city this March, but fighting continues nearby.
The Russian defence ministry said the frigate Admiral Essen and the submarine Krasnodar had fired Kalibr cruise missiles at "shelters" east of Palmyra, where a group of heavily armed militants previously deployed in Raqqa were based.
"All the targets were hit," it added.
The US, Turkish and Israeli militaries "were informed in a timely manner of the missile launches through existing communication channels".
Earlier this month Russia agreed with Iran, another Assad ally, and Turkey, a key backer of the opposition, to establish "de-escalation" zones in western Syria in an attempt to shore up a cessation of hostilities between the government and rebels.
IS and the rival al-Qaeda-linked alliance, Hayat Tahrir al-Sham, are excluded.
A Russian warship and submarine in the Mediterranean have fired four cruise missiles at so-called Islamic State (IS) positions in central Syria.