New Zealand scored three late tries to beat South Africa 24-21 but the Blitzboks were less than impressed with the Australian referee who gave nine penalties to the hosts and just one to South Africa in the final.
O'Brien, son of former New Zealand referee Paddy O'Brien, also sin-binned Rosko Specman in the second half.
South African website Supersport.com reports that O'Brien met with South Africa coach Neil Powell on Wednesday in Sydney ahead of this weekend's Sydney Sevens.
World Rugby Sevens assessor Tappe Henning also attended O'Brien delivered a "heartfelt" apology for the way he refereed the final.
Powell told Supersport.com the team had accepted it and moved on.
"I sat with him and we went through the second half of the game and he explained his decisions. It was really honest and open, and I think he realised at times he had made big mistakes. I think his apologies were sincere," Powell said.
"He apologised to me for the way he refereed the game."
