The South Africans, who were given a straight passage into the final of the men's 4x400m Olympic relay, finished eighth in London on Friday night, setting a season's best time of 3:03.46.
Reinstated into the event after a successful appeal for obstruction in Thursday's heat, South Africa trailed from the start in the final.
Double amputee Oscar Pistorius ran the last leg of the relay ending his historic appearance at the able-bodied games.
South Africa were the last team to cross the line as Cuba did not finish.
Bahamas set a national record for the gold medal in 2:56.72, followed by United States in 2:57.05.
Trinidad and Tobago took the bronze in a national record time of 2:59.40.
Thursday's appeal came after Ofentse Mogawane, running in the second leg of the relay heat, tripped when Kenya's Vincent Mumo Kilu cut in front of him.
Both athletes fell to the ground and, while the Kenyans were disqualified after completing the race, Mogawane was unable to continue.
Video evidence working in South Africa's favour meant they were granted the ninth spot in the final.
LJ van Zyl replaced Mogawane in the final, running with Shaun de Jager, Willie de Beer and Pistorius.
Earlier, South Africa's Tiffany Kruger failed to qualify for the semifinals of the women's K1 200m canoe sprint.
She finished last, in seventh place, in her heat in a time of 46.122 seconds, four seconds off the Ukranian winner, Inna Osypenko-Radomska.
The South African was the only participant in her heat not to qualify for the semifinals.
In swimming, Troyden Prinsloo finished 12th in the men's 10km marathon.
He finished in a time of one hour, 50 minutes and 52.9 seconds (1:50:52.9), nearly a minute behind Tunisian winner, Oussama Mellouli.
Mellouli bagged the gold medal ahead of Thomas Lurz of Germany and Richard Weinberger of Canada.
Prinsloo said he was pleased by his result and hoped to better his performance ahead of the 2016 showpiece.
"It was very tough. These guys were flying. I'm happy with 12th", Prinsloo said.
"It was a great experience and hopefully I can get the funding to focus on this (event) for Rio 2016."