The 57-year-old Serbian will be replaced by Brazilian Sebastiao Lazaroni, who had been coaching Qatar SC in the domestic top flight.
Rajevac, who led Ghana at the 2010 World Cup, had taken over as Qatar boss following Bruno Metsu’s dismissal after the 2011 Asian Cup, where they reached the quarter-finals as hosts.
However the Serbian failed to impress as Qatar boss with recent losses to India and Vietnam prompting the QFA to move to replace him.
Qatar, who face Iraq on Wednesday, did progress to the third round of World Cup qualifiers under Rajevac, where they were drawn in Group E to face Iran, Bahrain and Indonesia.
Lazaroni, who coached his native Brazil at the 1990 World Cup and more recently won the 2009 Qatar Coach of the Year award, will be in charge for those upcoming fixtures.