Previously, the U.S-led coalition had downed Iranian drones in the area, considering them hostile because they dropped ammunition near a base where USA troops operated alongside allied Syrian opposition fighters.
"The senior commander of the Military Advocates Group, Lieutenant General Valeriy Asapov, was at the command line of the Syrian troops, where he helped to run the release of the city of Deir Ez Zor", a ministry message said.
"A representative of United States command in Al Udeid, Qatar, was notified in severe form that attempts to attack from districts where SDF fighters are located will be repelled", he said.
SDF fighters captured the war-torn country's largest gas field, Koniko, from IS militants on September 23.More news: Target's pay hike could be especially beneficial for North Carolina workers
An global human rights group says two airstrikes by the USA -led coalition on northern Syria earlier this year killed 84 civilians, including 30 children.
Moscow denied this and said Syrian troops and Russian forces came under fire from SDF positions, warning the U.S that it would retaliate if the shelling was repeated.
A spokesman for the USA -led coalition, Colonel Ryan Dillon, said rounds had hit in the area around the SDF but he could not confirm they were fired by Russian Federation.
The assaults by the Russian-backed Syrian army and the US -backed SDF have at times raised fears of clashes that could stoke tensions between the competing world powers.More news: The best Sony Xperia XZ1 and XZ1 Compact deals for September 2017
Earlier this week, Syrian troops crossed into parts of east bank but have concentrated their operations mostly on the west.
A statement issued by the Syrian Democratic Forces said two other fighters were wounded in Monday's strike in the eastern province of Deir el-Zour. Contacts were increasing to avoid confrontation, he said. Together with Asapov, that brings the overall death toll of Russian servicemen in Syria to 37.
The convergence of the rival offensives has increased tensions in Deir al-Zor.
US-backed Syrian fighters seized a second district of Raqa and launched a renewed assault on a base north of the city, as they pursued an offensive against the Islamic State group.More news: Niasse: I've always kept fighting for my place