"This is my last international competition and I'm happy passing on the baton of African athletics to Uchenna (Emedolu) because he and the new generation of sprinters will represent the continent well," the 36-year-old told reporters.
Nigeria's Emedolu won the 200 metres in 20.42 seconds ahead of second-placed Fredericks (20.43), who holds the African record of 19.68 seconds set at the Atlanta Olympics in 1996.
"I wanted to bow out with the gold medal at the African Games but I reckon I had to run fast at the age of 36 to achieve it," said a disappointed Fredericks.
The Namibian, whose decision means he will miss next year's Olympic Games in Athens, was regarded as one of the great African sprinters but he never won an Olympic title in his career after finishing with silver and bronze medals.
However, he did win the 200 metres gold medal at the world championships in Stuttgart, Germany in 1993 and also collected three silver medals at the worlds at that distance.
Fredericks said his next vocation will be organising coaching clinics in Africa, starting in his native country.