كتب : Omar AbdelAziz
South Africa finished second in Group B, just one goal ahead of the young Pharaohs after both teams leveled on six points.
Nigeria, who beat Ivory Coast 3-0 in the other group game, claimed top spot on goal difference as well after they also amassed six points.
Ahli Dubai striker Mohamed Talaat scored two first half goals for Egypt, including a superb volley before the break.
But Thulane Ngcepe scored the vital goal for the South Africans in the 70th minute, capitalizing on a rare error from keeper Mohamed Abou-Gabal.
Nigeria and South Africa reach the semi-finals and make it to the 2009 U-20 World Cup, which will be hosted by Egypt in September.