Hosts Ghana took an early lead just two minutes in through Benjamin Tsivanyo, but the Junior Elephants responded with a penalty converted by Abdoul Bamba while Ali Kone scored the winner with 20 minutes left to play.
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Earlier in the day, the Flying Eagles edged Niger Republic 4-3 in a penalty shootout after a goalless 90 minutes.
Goalkeeper Ebenezer Harcourt, who made a key save, was named Player of the Match. Nigeria are using the tournament as preparation for the FIFA U-20 World Cup in Chile, having qualified by finishing third at the U-20 AFCON in Egypt.