Rudolf Straeuli has quit as coach of South Africa along with SA Rugby managing director Rian Oberholzer.
Both had been under pressure over the Springboks' poor World Cup campaign which ended with a quarter-final defeat by New Zealand.
Straeuli's role was further undermined by news of a pre-World Cup military-style boot camp and a racism row.
Officials said the pair had resigned on "mutually acceptable" terms.
Straeuli's role in organising Kamp Staaldraad [Camp Steel Wire] was played down by Songezo Nayo, SA Rugby's acting managing director.
The so-called team building session saw players, among other things, forced naked into a freezing lake to pump up rugby balls under water.
"Whilst SA Rugby continues to distance itself from KampStaaldraad, the board accepted that during the camp, which was conducted by the organisation employed to run the camp, Straeuli together with other members of the management team were merely observers," said Nayo.
Oberholzer said he was stepping down because he felt South African rugby needed new leadership.
"At a certain stage a person gets stale in this sort of job and the organisation needs a new man to come in with fresh ideas," he said.
The 40-year-old Straeuli was appointed in March last year after his predecessor, Harry Viljoen, quit following one of South Africa's most disappointing seasons ever.
But under Straeuli's charge the Springboks won only 12 out of 23 matches, another disastrous run which included an ugly 53-3 loss to England at Twickenham last November.
The side were then embroiled in a racism row before the World Cup when a white player, Geo Cronje, refused to share a room with a black player, Quinton Davids.
South African Sports Minister Ngconde Balfour appointed a commission of inquiry to investigate racism in rugby, but it was postponed until after the World Cup.