Mr Markgraaff said he had quit in the interests of South African rugby and of national reconciliation. "I'm not making any excuses," he said "I was very emotional at the time. I apologise to the black people of this country and to the whites for causing them embarrassment."
The recording of a conversation between a rugby official and a player was allegedly made in October during the national outcry about Mr Markgraaff's axing of Francois Pienaar, the popular team captain.
The tape, aired on SABC television on Monday night, despite threats of court action, became public three days after the government launched an investigation into alleged mismanagement and racism in the Afrikaner-dominated sport. Louis Luyt, the controversial president of the South African Rugby Football Union (Sarfu), is refusing to co-operate with the inquiry.
Few will regret Mr Markgraaff's downfall. Along with Dr Luyt, he became a national hate figure over- night for his treatment of Pienaar.
The resignation is another body blow for a sport which just two years ago held the promise of a social miracle. Every South African remembers the moment in 1995 when Nelson Mandela, sporting a Springbok shirt - for so long a symbol of oppression to blacks - passed the Rugby World Cup to Pienaar.
That moment marked more than South Africa's triumphant return to the international arena after years of sporting isolation. Yesterday, Mr Markgraaff apologised specifically to President Mandela.
Mr Mandela's gesture was an inspired move in South Africa's quest for racial reconciliation. In the run- up to the 1994 democratic elections, the rugby terraces had become the stage for ugly racist displays of white defiance at the coming political change. In embracing the sport, Mr Mandela indicated he believed it now had the makings of a truly national game.
Pienaar, like Mr Mandela, show-ed vision. He encouraged the team - all white bar one Coloured player - to learn the Xhosa words to Shosholoza, the stirring black miners' song which Mr Mandela sang during his years of hard labour on Robben Island and until then the anthem of predominantly black football fans. But the intoxicating optimism about the future of rugby - and racial harmony in South Africa- finally evaporated with Pienaar's sacking.
Critics, some from the ranks of the Coloured rugby union which merged with white rugby bodies after the fall of apartheid, claimed the sport was still being run by a cabal, which through racism and sheer love of power was doing little to open the sport up to blacks. How had cricket managed to make an impact in the townships when rugby had failed so dismally, it was asked.
Brian van Rooyen, a Coloured rugby, official challenged Dr Luyt for the presidency of the Transvaal Rugby Union in the wake of Pienaar's sacking. He lost but promised to continue his fight to make the management of rugby transparent. "I want to pave the way for a team that my sons might one day play for," he says.
Pienaar left South Africa after his sacking to join the English club Saracens. Mr Mandela invited him over for a farewell lunch. Since then, those who used the national out- cry to focus attention on the wider shortcomings of the game have been working quietly behind the scenes.
The tape is connected with a 500- page dossier Mr van Rooyen has just handed over to the government, questioning, among other things, the payment of commissions on rugby sponsorship and television deals. The government has since launched its inquiry.
Yesterday morning Mr Markgraaff was still holding on at his farm in Kimberly while Dr Luyt was insisting that there was no room in rugby for racism and that action would be taken against Mr Markgraaff if indeed he made the remarks.
However, Mr Markgraaff's resignation is almost certainly not the end of the matter.
The critics of Sarfu and Dr Luyt are just warming up. If Mr van Rooyen, who claims he has been threatened since he presented his dossier, has his way, Mr Markgraaff will not be the only official to be released to spend more time with his family.
The ANC has said that the tape reinforces "the perception that conservative elements within Sarfu are resisting the transformation of the union into a non-racial society".
It is a trend that is not confined to the rugby field.
South African sports commentators believe that if the ANC has lost patience it is no surprise.
"The fact is that Sarfu has done very little to transform rugby," said one South African sports writer.
"Since the world cup they have got rid of the more liberal elements at the top and retreated back behind the laager."
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