The Portuguese, who was 18 months into a two-year contract, took over from Gernot Rohr following the 2012 African Nations Cup during which hosts Gabon were eliminated on penalties by Mali in the quarter-finals.
"I have told Paulo Duarte that he is no longer national coach," interim FEGAFOOT president Dieudonne Likouni Ndoumbou was quoted as saying on the federation's website.
"We are working on his replacement. An announcement may take place in a few days," he said, adding that Duarte would remain national technical director until further notice.
Gabon, who have never played at the World Cup finals, finished third in qualifying Group E behind Burkina Faso and Congo.
Five African teams will qualify for next year's World Cup in Brazil after the playoffs scheduled to take place on October 11 and November 15.