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The hosts and Algeria played out a goalless draw on Monday to send both sides into the quarter-finals from Group A at the expense of Mali.
Angola finished top on five points with Algeria second on four.
Stephen Keshi's side finished level with Algeria after beating Malawi 3-1 on Monday but were squeezed out having lost 1-0 to the Desert Foxes last week.
Angola and Algeria went at each other's throats in an open first half at the 11 November stadium but when news filtered through from Cabinda that Mali were fully in control the second half turned into a dreary affair with neither team prepared to take any unnnecessary risks.
That attitude incensed the Mali team who have written to organisers the Confederation of African Football (CAF) to officially complain.
"We are lodging a vehement protest against the behaviour of the Algeria and Angola teams," the Mali Football Federation president Boubacar Thiam wrote in the letter, a copy of which has been seen by AFP.
"In fact the second half of this game was a total non-match, the two sides systematically refusing to play in order to maintain the score at 0-0 which was sufficient for qualification."
He continued: "This anti-sporting behaviour is contrary to the ethics and the fair-play policy put forward by FIFA and CAF must condemn it with the utmost vigour.
"It does a disservice to African football and to the game in general.
"We hope that CAF will take the necessary disciplinary measures."
Thiam cites as a precedent for his protest a similar incident at the Africa Cup of Nations Youth Championships in 2001 match against Cameroon and Egypt who were made to replay a match after a scoreless draw.
The notion that Monday's draw had been 'arranged' by Angola and Algeria before kick-off was strongly denied by Algeria coach Rabah Saadane and Angola captain Kali.
Saadane told Monday's post-match news conference: "I don't accept at all that this was a fixed match and that we had some sort of agreement with the Angolan team to play for a draw."
Kali was asked if he had had any contact with his opposite number, Algeria captain Yazid Mansouri, to as a journalist put it "arrange a draw".
Kali shook his head dismissively, replying: "It's wrong to insinuate that I met the Algerian captain to talk about fixing this game - journalists in Angola insinuate a lot of things and bring up a lot of negative points, it's wrong. I had no contact with the Algerian captain."
Saadane was Algeria assistant at the 1982 World Cup when Algeria were victims of the infamous draw between Austria and the then West Germany which saw those two neighbours progress to the second round at the expense of the Algerians.
