Competition hosts Ivory Coast emerged as 2-1 winners in extra-time of their quarter-final clash which has been marred by the post-match antics.
Mali won a corner deep into stoppage-time following Oumar Diakite's eventual late winner, with referee Adel blowing for full-time moments after.
He was surrounded by angry Malian players seconds later, with Traore shown a straight red card for his angry protests in the face of the Egyptian match official.
And footage shows Adel pushing the Real Sociedad star in self-defence as tensions ran high at the end of an action-packed match.
Some of the Malian coaching staff had to step in and take their players away from the official as they exit at the quarter-final stage.
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Adama Traore missed a penalty for Mali in the 17th minute, but they eventually took the lead in the second half thanks to Nene Dorgeles' stunning curling effort.
As the clock ticked down, it looked as though the country who are 51st in the world rankings were set to reach the semi-finals.
However, Simon Adingra fired in the equaliser for Ivory Coast in the 90th minute to ensure extra-time decided the winner.
The hosts then sealed their spot in the last four when Diakite found the back of the net in the second minute of stoppage time.
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Ivory Coast's hero was then sent off for a second yellow card though after taking his shirt off in the celebrations.
The hosts will now face DR Congo in their semi-final on Wednesday night, with the winner of Cape Verde and South Africa playing Nigeria in the other tie.
Incredibly, Ivory Coast only advanced through to the knockout stages as being the best fourth-best third-place team in the groups.
They had sacked boss Jean-Louis Gasset while their fate was uncertain, with Emerse Fae brought in to be the Elephants' caretaker.
Ivory Coast then knocked out holders Senegal in the Round of 16 on penalties having equalised in the 86th minute.