The ministry said the targets were destroyed. The Syrian Government has praised several times the contribution in the fight against terrorism by countries such as Russian Federation and Iran, along with the forces of the Islamic Resistance Movement of Lebanon (Hezbollah).
The militants control less than half the city and are encircled on three sides with their backs to the Euphrates River.
Assad's forces are now attempting to drive the terrorists out of the city, which is one of their last strongholds in Syria.
Meanwhile, U.S. -backed Syrian forces are advancing in the surrounding province from the east and north.
The Velikiy Novgorod and Kolpino are two of Russia's latest Varshavyanka-class stealth submarines, and joined the Russian Black Sea fleet late past year.
The country has repeatedly fired salvos of such missiles, from both the sea and mainland Russian Federation.
In this strike, the missiles were aimed at IS command points, communication hubs and arms dumps southeast of the city of Deir el-Zour, where Syrian troops and allied militias are battling the extremists.
As their so-called Caliphate collapses, ISIS has launched and claimed responsibility for a series of terror attacks overseas, including three in Britain this summer.
The deal reached at the end of August allowed hundreds of militants and their families to relocate to Boukamal, an Islamic State-held Syrian town near the Iraqi border, in exchange for Islamic State-held prisoners and the remains of Lebanese soldiers captured in 2014. On Thursday, a captive Hezbollah fighter was released.