The SABC reported on Thursday morning that his father, Bert le Clos, had confirmed that his son had withdrawn so that he might focus on his efforts in the 100m butterfly final.
This was after Le Clos on Tuesday won the gold medal in the 200m butterfly final on Tuesday evening.
Bert le Clos said his son believed he would have a better chance at another gold medal if he withdrew from the event.
Le Clos only just made it into the final after finishing fifth in his semifinal heat with a time of 1:58.49.
America's Ryan Lochte finished first overall in a time of 1:56.13.
South Africa's second gold medallist at the London games after Cameron van der Burgh took gold in men's 100m breaststroke final, Le Clos finished fifth on the 400m individual medley final on Saturday with a time of 4:12.13.
Le Clos (20) has said he approached the London Olympics with some anxiety at the thought of competing against the world's greatest swimming competitors – in particular his schoolboy idol, American swimmer Michael Phelps.
After winning gold in the 200m butterfly, pushing Phelps into second, Le Clos paid homage to his hero, tweeting on Wednesday: "@MichaelPhelps it was such an honour to race u last night, thank u for being such an inspiration to me and many others, ur the greatest!"