Coach Jake White told the after-match press conference that the Springboks, who suffered the second worst loss in their history, lacked fight.
"There's nothing much you can say after you lose like that. This really was a poor performance by the players.
"Australia played very, very well, but I thought we would have been more competitive."
White was critical of referee Paul Honiss' penalising of South Africa's rush defence.
Captain John Smit was hopeful of a much improved performance in Wellington.
"This obviously hurts a lot. We haven't been beaten like that in a long time, but we have to believe we can turn things around," he said.
Australian captain George Gregan said: "South Africa are a proud rugby nation so to beat them 49-0 is pretty special.
"We've probably had a few chances in the past to really put them away but this is the first time we've actually done it."
Coach John Connolly was happier than after the opening game against the All Blacks but was not getting carried away.
"We played well but we still can't get carried away because we've still got some things to work on.
"We took the foot off the pedal in the second half and I think we all realise we left a lot of tries out there."
Criticism of the effort was immediate in South Africa with prominent rugby writer Dan Retief saying on Supersport.co.za, "The Boks were embarrassingly inept; at times resembling a team from the backwaters of rugby rather than one of the world's top teams.
"There was almost nothing positive that could be taken from an aimless, desultory performance that is sure to rebound on coach Jake White as the ill-conceived pursuit of his personal objectives will be held to have side-tracked the Boks' preparation and concentration."