Gomolemo Kekana's stunning right-footed strike from outside the box found the top left corner, giving South Africa the lead just 20 minutes before the whistle.
Morocco's U-20 team reached the final after edging hosts Egypt 1-0 in the semifinals, while South Africa triumphed over Nigeria by the same scoreline.
All four semifinalists have now qualified for the FIFA U-20 World Cup in Chile later this year.
The Young Atlas Lions applied early pressure but squandered several chances, with Fouad Zahouani and Abdelhamid Aït Boudlal both failing to convert.
Sunday’s win marked revenge for South Africa, who had lost to Morocco in the 1997 U-20 Africa Cup of Nations final, where the match ended 1-0 in Morocco's favour.
Egypt’s U-20 team missed out on a podium finish in the continental tournament after losing 4-1 in a penalty shootout to Nigeria, following a 1-1 draw in regular time at the Air Defence Stadium in Cairo early on Sunday.
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