The Ugandan Football Federation said in a statement that it had"mutually agreed" to end the Frenchman's contract.
Desabre is the second coach to part company with his team at the tournament after hosts Egypt sacked Javier Aguirre immediately following their shock elimination against South Africa in the round of 16 on Saturday. Uganda, playing a bold attacking game, beat Democratic Republic of Congo in their opening game, outplayed hosts Egypt despite losing 2-0 and gave Senegal a run for their money in the round of 16 before losing 1-0.
"FUFA recognises the contribution by Mr Desabre for the improvement of the sporting and professional organisation of the Uganda Cranes inclusive of qualification to the AFCON 2019 Finals and also to the Round of 16," said the statement.