He was detained on Wednesday at Johannesburg's OR Tambo International Airport after an anonymous tip-off.
"The 28-year-old male, who was in transit from Namibia to board a South African Airways flight to Hong Kong, was immediately arrested," the organised crime police unit said in a statement.
The horns, weighing 43 kilograms (95 pounds), were valued at around 6.6 million rand ($467,000, 441,000 euros).
He is due to appear in court on Friday.
Southern African countries are battling increased poaching levels. The trade is fuelled by organised syndicates mainly from Asian countries.
South Africa, which has the largest rhino population worldwide, has been hit the hardest, with 1,200 slaughtered last year alone.
Most of them were killed at the Kruger National Park, the country's premier safari destination.
The illegal trade is driven by huge demand in Vietnam and China, where it is believed to have medicinal powers curing everything from hangovers to cancer.
The belief has been scientifically proven to be false.
The horn is also crafted into prized ornaments.
In August, another Hong Kong-bound Chinese man was arrested at OR Tambo airport with 10 rhino horns and carved ornaments.
Reuters
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