SASCOC Chief Executive Officer Tubby Reddy described the CAS ruling as a sad day for them.
"It is indeed a very sad day for us as a country to be instructed to select an athlete into Team SA against our will, but being a disciplined member of the Olympic Movement, we have no option but to adhere fully to this decision.
"The CAS has unfortunately ruled in favour of Alex Peternell and has instructed both the South African Equestrian Federation (SAEF) and ourselves (SASCOC) to include this athlete in our team," he said.
This comes after the British based South African Peternell approached CAS after SAEF turned down his nomination for the Olympic Games as they had their own preferred rider, Paul Hart.
Peternell is the first South African to have competed at Badminton and Burghley.
This was the second attempt by Peternell to take SASCOC and the SAEF to CAS.
Reddy further said: "As we all know, this athlete has been based in the United Kingdom for the last 11 years consecutively and we have now been instructed to include him in the equestrian discipline of eventing."
With regard to Hart, the SASCOC boss said they have tried persistently to support him in his quest for Olympic representation -- even challenging CAS twice, which indicated their belief that his selection was the fair thing to do.
"It is with regret that one of our loyal countrymen, Paul Hart, has to bear the brunt of this sad situation. This decision is unfortunate as it forces upon the South African public an athlete that they do not necessarily recognise and one that they do not necessarily support," Reddy said.
He added that it was abundantly clear from the comments posted on their official website that the South African public has continuously supported Hart as the preferred athlete for selection.
"Unfortunately with this ruling of CAS, we cannot deviate in any way ... as this ruling gives a clear indication that the selection of Peternell has been made by CAS and we are now implementing their decision.
"While this whole affair is regrettable, for the sake of the Olympic Games it is important to move forward and focus our energies on the job on hand and concentrate on our team's preparation," he said.