In a match that Amajita had to win to qualify for the semifinals of the eight-team tournament while also automatically qualifying for the World Cup later this year, it was once again a defensive error that saw them lose their second match of the tournament.
On the stroke of halftime, goalkeeper Ronwen Williams made a meal of a back pass that landed on the path of Egyptian striker Mohamed Hamdy to lobby over the head of the error prone keeper in the 45th minute.
This means that the highly-rated North Africans and Mali from this group make it through to the next stage and will also be two of the continent's four representatives in Colombia, with South Africa missing out after having qualified for the last tournament in 2009.
Although South Africa are strong in attack, their Achilles' heel has been in defence, especially in the goalkeeper department, where there were mistakes in all three of their matches with the preferred choice for the first match against Mali, Tawfeeq Allie's blunder proving costly as the team went down 4-2.
However, Williams will get some credit for a couple of saves midway through the second-half that kept South Africa in play where he denied Salah and midfielder Ahmed Hagazi.
The South African coach Maqsood Chenia had started the match with a 5-4-1 system against his technically brilliant opponents and in the first half came close to finding a goal with a pinpoint header from striker Lucky Nguzana being tipped over the post by Ahmed Al Shanawy in the Egyptian goal.
In the second half, Hamdy could have found a second shortly before the hour mark until he shot wide of goal with just Williams to beat while Mohamed Salah's attempt at curling the ball also went narrowly past the post.
Amajita began a late surge at finding the two goals they now required to qualify, and came close when captain Philani Khwela rattled the network with a sublime shot on the hour mark with goalkeeper Al Shanawy beaten.
The home team will feel that they were denied a legitimate call for a penalty when winger Jabulani Ncubeni was fouled in the penalty box in the dying moments of the game.