"I can tell you Mali have lodged a complaint to CAF regarding the match between Angola and Algeria," Mali official Alassane Souleymane told Reuters on Tuesday.
Mali federation general secretary Boubacar Thiam said in a letter to CAF, of which Reuters obtained a copy, that the second half between Algeria and Angola broke the "fair play" policy.
Mali missed out on a quarter-final place despite beating Malawi 3-1 in their final Group A game on Monday, the goalless draw between hosts Angola and Algeria meaning both those teams qualified.
Angola finished top on five points, one ahead of Algeria and Mali. Algeria advanced thanks to tournament rules which take into account head-to-head records first rather than goal difference. Algeria had beaten Mali 1-0 last week.
"We vehemently protest against the behaviour of the Algerian and Angolan teams during the final game of the group phase of the African Nations Cup," Thiam said in the letter.
"The second half of this game looked a hardly contested one, with both teams systematically refusing to play and trying to keep the 0-0 scoreline that would qualify them both.
"This behaviour goes against ethics and fair play advocated by FIFA and CAF. It must be condemned with the greatest energy. It does not honour African football and football in general."
CAF were not available for comment.
Algeria, who were eliminated in the first round of the 1982 World Cup after West Germany and Austria appeared to aimlessly kick around the ball for most of their final game, denied any wrongdoing.
"There was no agreement with Angola. We never could do such a thing," said Algeria coach Rabah Saadane.
"Algeria were the victim of an agreement between Austria and (West) Germany in 1982. I can assure you that Algeria and Angola did not do it."
Algeria midfielder Karim Ziani said: "Of course we knew the score (of Mali v Malawi), we knew a draw would be enough and against a strong side like Angola it was safer to stay behind and in control."
