The forward suffered a pulled thigh muscle in Tuesday's goalless draw with Zambia and could be out for up to two months.
Traore said he felt the injury as he attempted an early cross and he was taken off in the 11th minute.
The 24-year-old from French club Lorient overcame an ankle injury to make the squad and scored three goals in the first two matches of the tournament.
Burkina Faso surprisingly finished top of their group and will play Togo or Tunisia in the quarter-finals in Nelspruit on Sunday.
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