All targeted objects were hit, the ministry said. This isn't the first time Russian Federation is stepping up to the plate, as they have been backing Syrian President since 2015.
They said that while the militants still control rural areas outside the city and the border with Iraq, they are now encircled by Syrian troops from three sides, with their backs to the Euphrates River.
The Syrian Democratic Forces (SDF), a US -backed alliance of mostly Arab and Kurdish fighters, meanwhile have also launched a separate assault in Deir al-Zor province, which has become Islamic State's last major foothold in Syria.
The Velikiy Novgorod and Kolpino are two of Russia's latest Varshavyanka-class stealth submarines, and joined the Russian Black Sea fleet late a year ago.
Advanced stealth technology is coupled with 18 torpedoes and eight cruise missiles, which Russian Federation claims will allow the craft to strike land, sea and air targets.
Syrian government forces broke a three-year Islamic State siege on parts of the provincial capital, also known as Deir el-Zour, last week, and are now battling the extremists inside the city.
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. On Thursday, a captive Hezbollah fighter was released.
The convoy was stranded in the desert for about two weeks, even though reports claim that some of the vehicles were able to slip into the militant-held territory. Last week, the U.S-led coalition said it ended surveillance of the convoy after a Russian request.