The 53-year-old, who took over as the top Bulgarian club's head coach in December 2014, has had his contract cancelled through mutual consent, it said.
Stoev's departure, following Levski's home defeat on Tuesday which handed rivals Ludogorets a fifth successive league title, kept up the pace of a coaching merry-go-round at the ground which has often enraged fans and commentators.
Since Emil Velev took Levski to the league title in 2009, there have been 18 changes in all with coaches often being given their marching orders only to return to their old jobs a few seasons later.
"Levski thanks Stoycho Stoev for his work and wishes him success in the future," the Sofia-based side said in a statement.
Levski's 3-2 defeat by Lokomotov Plovdiv on Tuesday leaves them second in the standings with three matches of the season remaining, but 14 points behind Ludogorets.
(Reporting by Angel Krasimirov; Editing by Richard Balmforth)
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