Keshi contract not renewed by Mali
"The federation acknowledges the end of the technical staff's contracts," it said in a statement on Thursday.
Nigerian Keshi's contract runs out at the end of the month.
Mali finished third in Group A level on points with Algeria behind hosts Angola but were denied a quarter-final place because of their head-to-head record with the Algerians.
They were also eliminated early last year in the 2010 World Cup qualifiers, despite being considered credible favourites to qualify for the tournament in South Africa.
Keshi had been in the post for two years. The former Nigeria World Cup captain had previously coached Togo.
He had predicted his departure after leaving for Angola, telling reporters conditions around the national team would have to change if he was to continue.
Mali striker Frederic Kanoute said last week he was also considering ending his international career.
Mali's federation said the search for a new coach would begin immediately.