Kempson was banned for four weeks for a late tackle on Australian number eight Toutai Kefu while Botha received an eight-week ban for "attacking the face" of Wallabies' hooker Brendan Cannon.
The bans, which followed a marathon six-hour hearing in Brisbane yesterday, mean the pair will miss South Africa's final Tri-nations match against New Zealand in Dunedin on Saturday but will be eligible to resume playing before the World Cup, starting on October 10.
Kempson and Botha were ordered to appear before the three-member judiciary panel after Australia coach Eddie Jones lodged an official complaint with the citing commissioner Steve Hinds.
A furious Jones accused the South Africans of a deliberate and pre-meditated campaign of foul play against his players, describing their actions as "disgraceful".
Kefu was rushed to hospital and later diagnosed with spinal concussion after being felled from behind by a swinging arm from prop Kempson and is in doubt for Australia's final Tri-nations match with the All Blacks.
Australian hooker Brendan Cannon claimed he was bitten and eye-gouged by a South African player, later identified as replacement lock Botha.
Cannon appeared at the tribunal to give evidence against Botha, who admitted touching the Australia's face but said there was no malicious intent.
The panel ruled that Botha had acted recklessly but not deliberately, saving him from a possibly longer ban.
Kempson received a four-week ban for the less serious offence after the panel rejected his claim that his high tackle on Kefu was not dangerous.
Kempson, who had earlier been sin-binned for tripping Australia captain George Gregan, flattened Kefu when he struck him from behind after he had passed the ball on to Phil Waugh to score a try.
The South African players and management did not comment on the outcome of the hearing after Sunday's marathon sitting but are entitled to an appeal.
South African rugby has been tainted by a series of violent incidents since the Springboks were readmitted to world rugby in 1992.
In 1993, France captain Jean-Francois Tordo required 50 stitches to his face and two hours of plastic surgery after being raked by a boot in an international against South Africa.
A year later, Springboks prop Johan le Roux received the longest ban in rugby history when he was suspended for 19 months after biting the ear of All Blacks captain Sean Fitzpatrick during an international.
In 1998, South African flanker Wickus van Heerden was banned for 18 months for biting New South Wales prop Richard Harry during Super-12 match in Sydney. The ban was later reduced to 12 months on appeal.
Then last year, South African lock Jannes Labuschagne was suspended for 23 days for a high tackle on England flyhalf Jonny Wilkinson at Twickenham.