Uganda lost 1-0 to Senegal in Cairo on Friday after reaching the knockout stage of the competition for the first time since finishing runners-up in 1978.
The Ugandan federation said it would confirm the new coaching staff "in the near future" after Desabre left with five months of his contract still to run.
"FUFA is grateful for Mr Desabre's contribution to the sporting and professional development of the Uganda Cranes, including qualifying for the finals and the knockout stages of CAN-2019," FUFA said in a statement.
The 42-year-old Desabre had been in charge of Uganda since signing a two-year deal in December 2017.
Desabre could not be reached for comment.
Ahead of the Cranes' loss to Senegal on Friday, the players had staged a three-day strike over unpaid dues by FUFA.
Ugandan President Yoweri Museveni will host the national side at an official function on Monday.