The two submarines launched seven Kalibr missiles against targets located some 500-650 kilometers away, the Russian Defense Ministry said adding that the target's destruction had been proven by intelligence.
Russian Federation has provided military backing for Syrian President Bashar Assad's forces since 2015.
"The strikes targeted control posts, communication centers as well as ammo and munitions storages in the ISIS controlled areas to the south-east from Deir ez-Zor", the agency said.
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 President Bashar al-Assad in a recent message to Iran's Supreme Leader Ayatollah Seyyed Ali Khamenei has thanked the country for its role in lifting the siege of Deir ez-Zor city, an Islamic State stronghold in eastern Syria, IRNA reports.More news: Cassini mission to Saturn
Meanwhile, U.S. -backed Syrian forces are advancing in the surrounding province from the east and north. The ISIS militants are now encircled by Syrian Military from three sides, with the Euphrates river on the back.
US -backed militias fighting Islamic State are not planning to enter the city of Deir al-Zor in eastern Syria, a USA military spokesman said on Thursday, reducing the chances of the American allies coming face to face with Syrian government forces.
Last week, aided by the intense aerial campaign, Syrian and allied forces managed to push their way toward the city, breaking a almost three-year siege on its troops on the western edge of Deir el-Zour. On Thursday, a captive Hezbollah fighter was released.
According to Britain-based Syrian Observatory for Human Rights head, Rami Abdurrahman, buses and vehicles carrying about 400 militants and civilians crossed into Deir el-Zour province on Wednesday, but no details were available about where the buses went.
U.S. Army Colonel Ryan Dillon, a spokesman for the U.S. -led coalition fighting Islamic State, told reporters that the battlefield was already congested and the plan was for the SDF to move down the middle Euphrates River Valley.