The federation said it had accepted a request from the 45-year-old coach to prematurely end his contract.
Three possible successors have been identified and the federation said a decision would be taken in the coming days, after they had been interviewed.
The three are Nabil Maaloul, who led Esperance to the African Champions League title in 2011, Khaled Ben Yahia and Maher Kenzari.
Tunisia failed to get past the first round after finishing third in Group D. At last year's Nations Cup, Trabelsi had led the side into the quarter-finals before Ghana knocked them out.
A former World Cup defender, Trabelsi was appointed Tunisia coach in March 2011. He is the first coaching casualty of this year's Nations Cup.