Traore pulled a muscle in his left thigh in the opening minutes of Tuesday's goalless draw with champions Zambia, which saw his side top Group C.
"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, holding an ice pack to his thigh, said: "For me the Nations Cup is finished. We were waiting to qualify for the quarter-finals for such a long time this injury has spoiled the enjoyment a little."
Traore it was who played a pivotal role in Burkina Faso's presence in the quarter-finals. The Lorient forward produced the stoppage time goal that saw them draw 1-1 with Nigeria, and then grabbed a double in the 4-0 rout of Ethiopia.
"At half-time last night my teammates came to see me, they told me that I shouldn't worry, that it was thanks to me that they had made it. They were right behind me, they were upset for me."
Tuesday's injury was bad luck, coming after his ankle sprain suffered in mid-December that almost cost him his place in coach Paul Put's squad for South Africa.
"I told myself it was going to be difficult (after his ankle problem) to play three consecutive matches," Traore continued. "Tuesday's game was my second start since Decemmber 19. The coach had planned not to play me for the whole match, unfortunately things worked out differently."
"I was quite upset, as personally I'd made a good start to the competition, I was feeling good. I'm disappointed, but that's the life of a footballer. Last night my club doctor at Lorient called me, he wants me to return to France for treatment - we'll have to see."
Burkina Faso will face either Togo or Tunisia in Sunday's quarter-final.