David Notoane's side managed just one goal in their four games at the tournament‚ through a stunning Teboho Mokoena free-kick before their semi-final exit at the hands of hosts Egypt.
Meanwhile, Ghana, who were in their first U23 AFCON since it's inception were knocked out at the last-four stage by Ivory Coast on penalties.
After a nervy start, South Africa took the lead through a Habib Mohamed own-goal as Luther Singh's effort deflected in off the defender in the 15th minute.
Mamelodi Sundowns forward Keletso Makgalwa had a perfect opportunity to make it 2-0 on the half-hour mark after being set up at point-blank range but he's hesitation offered Ghana a chance to clear their lines.
Notoane's charged took the lead into the break having dominated the latter stages of the half but were made to rue their chances as Ghana found an equaliser in the 50th minute.
Ghana XI: K. Baah; K. Fobi, H. Mohammed, Z. Fuseini, E. Sarpong, E. Lomotey, M.Agbekpornu, Y. Yeboah (C), E. Mensah, K. Owusu, S. Gyabaa.
SA XI: M. Mpoto; K. Johannes, T. Mukumela, T. Malepe (C), K. Mohamme, T. Mokoena, A. Dlala, G. Margeman, K. Makgalwa, L. Singh, L. Foster.