Traore pulled a muscle in his left thigh in Tuesday's goalless draw with Zambia, which saw his side top Group C. They are likely to face either Togo or Tunisia in Sunday's quarterfinal.
"Alain's chances of continuing in this Nations Cup are minus 10 percent," the team's doctor, Romaric Toe, told AFP on Wednesday.
"He pulled a muscle in his left thigh, and will undergo all the necessary examinations, but his competition I would say is over."
Traore said: "For me the Nations Cup is finished. We were waiting to qualify for the quarterfinals for such a long time this injury has spoiled the enjoyment a little."
The forward has played a huge role in his sides march to the quarterfinals when he scored the stoppage time goal that saw them draw 1-1 with Nigeria, and then grabbed a brace in the 4-0 rout of Ethiopia.
The injury comes after an ankle sprain in mid-December that almost cost him his place in coach Paul Put's Afcon squad.