Horner had led the team since its inception in 2005, guiding them to six constructors' titles and eight drivers' crowns.
His sacking follows a personal scandal last year involving allegations of inappropriate behaviour with a female colleague. He was cleared of wrongdoing after internal investigations and an appeal.
Laurent Mekies, previously from sister team Racing Bulls, has been named as his replacement as CEO of Red Bull Racing.
Red Bull's CEO of Corporate Projects and Investments, Oliver Mintzlaff, issued a statement thanking Horner for his "exceptional work" over two decades.