This weekend's third/fourth-place playoff started at a frantic pace, with South Africa taking the lead after just five minutes through Liam Jordan.
However, Guinea trailed for less than 120 seconds as they were gifted an equaliser, Katlego Mohamme miscommunicating with Sanele Tshabalala to head the ball past his own goalkeeper and into the back of the net.
South Africa were then dealt a big blow midway through the second-half as Aghmat Ceres needed to come off with injury, forcing coach Thabo Senong into making his third and final substitute.
Tshabalala then twice needed to be at his best to keep out Guinea with two brilliant saves, although the goalkeeper was soon left staring down a penalty after Tercious Malepe had committed a foul in the area.
And, Guinea made no mistake from the spot as Naby Bangoura fired home to snatch the win and bronze medal away from the South Africans.
South Africa: Tshabalala (GK); Katlego Mohamme; Aghmat Ceres (Thendo Mukumela 72'); Tercious Malepe (C); Siyabonga Ngezana; Grant Margeman; Wiseman Meyiwa; Liam Jordan; Sipho Mbule; Kobamelo Kodisang (Sibongakonke Mbatha 60'); Itumeleng Shopane (Luther Singh 53').
Unused subs: Mondli Mpoto; Khulekani Khubeka; Sandile Mthethwa; Notha Ngcobo; Khanyisa Mayo.