The reigning champions were knocked out after losing 1-0 to Morocco.
The Frenchman's decision to resign after 18 months in the job was announced by the Ivorian Football Federation (FIF).
The Elephants failed to register a win in Gabon, after draws with Togo and DR Congo and the defeat to the Moroccans.
The federation's statement praised Dussuyer's "professionalism, commitment and human quality", adding that "the appropriate measures will be put in place to find his successor".
Michel Dussuyer has stood down as Ivory Coast manager following his team's early elimination at the Africa Cup of Nations.