Smith, who made his international debut against Scotland back in 2003, started all three Tests against the Lions earlier this summer.
The 28-year-old then played a key role in his country's first Tri Nations triumph since 2004 as the Boks won all bar one of their tournament fixtures.
But Smith will play no part in South Africa's European tour this autumn, with the world's No1 side forced to take on France, Italy and Ireland without arguably their first-choice back-row forward.
Having been given the weekend off as the Cheetahs prepared to face the Sharks in the latest round of the Currie Cup, Smith had a freak accident while working on his farm.
And while Smith's absence is clearly a blow to Peter de Villiers and the Boks, it will have an even more immediate impact on the Cheetahs' hopes of reaching the play-off stages of South Africa's premier club competition.
The Cheetahs currently lie in fifth place in the standings; one position shy of a semi-final berth after Saturday's loss to the table-topping Sharks.
"It is a blow," Cheetahs assistant coach Hawies Fourie told rugby365.
"Juan damaged his medial knee ligaments. He will only be able to play in the Super 14 again next year."