Senegal emerged the winners from a chaotic final held at the Prince Moulay Abdellah Stadium with Papa Gueye netting a 94th minute winner after Brahim Díaz saw his Penenka penalty easily saved.
But all this happened after the Senegalese players left the field in protest under the orders of head coach Pape Thiaw before being called back by Sadio Mane.
Morocco protested te result and have now sensationally been awarded a retrospective 3-0 win and the title as AFCON winners.
"No one could have imagined such a statement two months after the final," said Le Roy on Africa Soccer.
"For years, all the refereeing decisions have been flouted by the CAF."
"You cannot build trust in African football if the outcomes on the field can be overturned months later without clear justification," the coach added.
Le Roy managed Senegal between 1988 and 1992.
Senegal has called for an independent corruption investigation after the Confederation of African Football stripped the country of its Africa Cup of Nations title and awarded it to Morocco, a decision it has strongly rejected.
Morocco have been officially crowned champions of the 2025 Africa Cup of Nations after a dramatic post-match ruling overturned the original outcome of the final against Senegal.
Belgian coach Yannick Ferrera has thrown his support behind the appointment of Mohamed Ouahbi as head coach of the Morocco national football team, insisting the move comes at the right time and poses no risk to the Moroccan tactician's career.
Mohamed Ouahbi has been appointed as the new head coach of the Moroccan national team, the Royal Moroccan Football Federation have announced.
