The 47-year-old has had his contract cancelled through mutual consent. Sergei Chikishev, who was in charge of the youth team, has been put in temporary control of the club. Kobelev took over as head coach in July 2015.
However Dynamo have picked up only one point from their last six matches.
They lost 3-0 to Moscow rivals Spartak 3-0 on Sunday.
With three matches of the season remaining, the side are in 12th place, one point off the relegation playoff zone.
Dynamo, who won the Soviet championship on 11 occasions, have never been relegated from the top flight during the Soviet Union or Russia.