Le Clos won gold in the men's 200m butterfly at the London Olympic Games when he pipped legendary American Michael Phelps, and also notched up a silver in the men's 100m butterfly.
He bagged a million rands and a luxury BMW car by securing the most votes from the South African public.
Other nominees for the award were Hashim Amla (cricket), Natalie du Toit (swimming), Siyabonga Nomvethe (soccer), Vernon Philander (cricket), Oscar Pistorius (athletics) and Caster Semenya (athletics).
Semenya was named the 'Sportswoman of the Year' after her silver medal in the 800m in London.
Pistorius got the 'Sportsman of the Year with a Disability' after becoming the first amputee runner to compete at the Olympics, with Du Toit was named Sportswoman of the Year with a Disability.
Cricket South Africa congratulated Philander for the honour he got.
"Vernon has been an inspirational member of the Proteas Castle Lager Test squad during the past year," said Cricket South Africa Acting CEO Jacques Faul.
"To become the fastest player to take 50 Test match wickets in more than 100 years is a phenomenal achievement on its own. But to do so in his debut year of Test match cricket is truly remarkable.
"To cap it all he was named Man of the Match in South Africa's Test victory at Lord's this year when the Proteas claimed the No.1 ranking in Test match cricket," he added.