Fleck had called van Rooyen a "dickhead that is f**king up South African rugby" and a "bloody racist" in the July issue of the magazine. In response, van Rooyen had sought to have Fleck arrested and extradited, on the basis that the magazine was also on sale in Britain.
Fleck's apology came via a SARFU press release in which he is quoted as saying,
"I sincerely apologise to Van Rooyen and his family for any distress or embarrassment that I have caused as a result of my comments.
"I now realise that my comments have not only offended Van Rooyen, but a lot of people.
"At the time, I did not give thought to the possible impact of my comments and admit that I acted irresponsibly.
"I would like to extend a personal apology to Van Rooyen at his earliest convenience.
"South African rugby are doing well at present, the Bok team has achieved success and I wish them the best for the future.
In response, Van Rooyen said: "Fleck has taken the correct step to apologise and, in his interest, as well as for the well-being of rugby in South Africa, I accept his apology.
"Furthermore, one sincerely hopes that the incident will reiterate the fact that individuals and publications should certainly be more responsibly-minded when publishing statements that could be perceived as derogatory, racist or defamatory."