Ghana surrendered top spot in Group B at the African Youth Championship after losing 1-0 to new leaders Mali on Sunday in Mbour in the final group phase match.
The Black Satellites needed a draw to head the pool after two wins against South Africa and Zambia.
Head coach Sellas Tetteh made four changes to the starting line-up and the gamble did not pay off.
Striker Benjamin Tetteh had recovered from a knee injury but was rested as a precautionary measure.
Ghana began the game the brightest with some bright inter change passes between Clifford Aboagye and Prosper Kassim to set up Samuel Afful but the latter fluffed his lines.
Mali took a surprise lead when Ichaka Diarra headed in a corner kick after goalkeeper Muntawaliku Siedu failed to punch it away.
The second half started with the same tempo with Mali midfield duo of Aboubacar Doumbia and Fousseyni Diabate overpowering Clifford Aboagye and Aseidu Attobrah.
The Malians could have put the game beyond doubt on the 80 minute but for a superb save from Ghanaian goalkeeper Seidu who pulled off a good save to deny Hamidou Traore when he was through on goal.
Aboagye made a good run into the Malian defense late on but goalkeeper Sory Ibrahimi Traore sniffed off the danger by coolly collecting the cut back.
The defeat for Ghana means they finish second in Group B and face Nigeria at the Semi-final stage on Wednesday.
Mali will play hosts Senegal in the second semi-final.
Story by Senegal/ JOY Sports/ Benedict Owusu
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