Thendo Mukumela slotted in at right-back in place of Thabiso Monyane, whilst Sipho Mbule and Kobamelo Kodisang started in place of Lyle Foster and Tercious Malepe for the South Africans.
South Africa threw a few punches of their own in the opening minutes, with a free-kick from Teboho Mokoena flashing wide of the post following the opening minutes.
The Egyptians dealt with every probably threat that came from the South Africans thereafter, with Luther Singh stopped in his tracks whilst attempting a crack at goal before halftime.
Neither side opted for changes during the interval, but the young South Africans made a promising start to the second period however still fired blanks in the final third.
Egypt broke the deadlock in the 59th minute when a handball resulted in a penalty kick which Ramadan Sobhi converted after sending Darren Johnson the wrong way.
David Notoane introduced more firepower with Foster coming in for Mbule five minutes later, as the Egyptians held the forth on virtually every compartment.
Singh threatened to level matters in the final eight minutes, though Singh saw his free-kick cracked the crossbar.
Abdel-Rahman Magdi went and forced himself down the right to rifle home a close-range shot two minutes later after the visitors failed to clear their lines.
Magdi had a double within the matter of five minutes when a howler from Johnson helped the former's probing attempt to an unguarded net.
South Africa will now have to play for third place and hope to qualify for the Olympic games through that route just as in 2016.