This was a match that Amajita had to win to qualify for the semi-finals but a defensive error cost them.
The goal was scored just before half-time when a back pass was intercepted by Egyptian striker Mohamed Hamdy who then lobbed the ball over goalkeeper Ronwen Williams to score.
Both sides missed many good scoring opportunities throughout the match due to poor finishing.
In the other game Mali and Lesotho shared the spoils in a 1-1 draw at Millpark Stadium in their final group stage match.
The Group A leaders Mali consolidated their place at the top of the standings after the draw, having won two games already.
Ballo Drissa scored for Mali in the 17th minute and seemed on course for a win before Mosiuda Christopher Boseka equalised for an impressive Lesotho in the 82nd minute.
Mali and Egypt advance from Group A into the semifinals and will both represent Africa at the 2011 Fifa Under-20 World Cup in Colombia later this year.
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