Jacques Nienaber’s team has not played a competitive fixture since beating England in the final in Yokohama in November 2019 to hoist the Webb Ellis Cup for the third time.
The withdrawal leaves New Zealand, Australia and Argentina to contest the Rugby Championship from 31 October.
Jurie Roux, the head of South Africa Rugby, said he was disappointed the Test team could not participate in the annual tournament.
"But the ongoing impacts of the pandemic in multiple dispensations mean we are unable to deliver a Springbok team without seriously compromising player welfare, apart from other logistical challenges," he added.
Resumption
New Zealand resumed rugby in June and Australia followed suit soon after. However the pandemic has forced a longer shutdown in South Africa.
Australia will face New Zealand in Sydney on 31 October to kick off the 2020 championship. The sides will play again on 7 November in Brisbane. Both teams will then take turns playing Argentina in Sydney and Newcastle.
Andy Marinos, chief executive of SANZAAR, which organises the championship, said: "SANZAAR recognises the challenges and adversity that the national unions have had to face this year due to the pandemic. It is a tribute to the unions in how they have been able to adapt.”
South African players face the prospect of no Test rugby until they host the British and Irish Lions in Soweto next July while the country’s rugby administrators will lose nearly 16 million euros of income by not taking part in the championship.
