Bok coach Heyneke Meyer gave credit to the Wallabies for a strong finish in Brisbane as the visitors started the Rugby Championship with a 24-20 loss.
For the second successive year, Australia snuck over with a try at the death as Tevita Kuridrani scored the match-winning try for the home team, awarded after a long deliberation between the referee and the TMO, adding to five-pointers by Adam Ashley-Cooper and Michael Hooper in a superb game on Saturday.
Springbok second-row Eben Etzebeth and outside centre Jesse Kriel, on debut, both scored their first Test tries for South Africa, while fly-half Handre Pollard slotted four kicks from five at goal, two conversions and two penalty goals.
With ten minutes to play, the Springboks were ahead by 20-10 before Hooper went over and then centre Kuridrani crossed for a converted try in injury time.
"It's heart-breaking to lose like that for a second year running in Australia, but we simply can't dwell on it and have to take some harsh but valuable lessons to heart," said Meyer, who refused the question the decisions to award a penalty and the subsequent try against the Boks at the death, while they were in control of the ball.
"Losing our captain early was tough and we finished the match with eight players who were playing in their tenth Test or fewer than that. It's not an excuse – we will all be better for it and we will have to look at ways to overcome this.
"Although we played some brilliant rugby at times, our execution also let us down and I think we left two tries out there, right at the end of the first half and midway through the second.
"We probably lacked some experience at the end when we needed to close the match, but we've said from the word go this season that we wanted to use our five matches in the build-up to the Rugby World Cup to get ready.
"We'll never accept defeat but I believe that we will take a lot from this match against a very experienced Wallaby team. Next week we have the All Blacks waiting in Johannesburg and we have to rise to the challenge.
Apart from injuries to Victor Matfield and Marcell Coetzee, Jannie du Plessis had to undergo a head injury assessment early on and was subsequently taken off the field in the 48th minute, while Francois Louw got a nasty cut to his mouth.
All the injured players will be re-assessed by the Springbok medical team in Johannesburg on Monday. Both Matfield and Coetzee will be in a race against time to be fit to face New Zealand next week.
"There were lots of hard knocks out there and all these injuries will certainly test our depth, but the guys next in line will have to show what they've got and stand up next week," said Meyer.
"We're already without experienced players such as Jean de Villiers, Fourie du Preez, Duane Vermeulen and Willem Alberts, but we always wanted to use the Tests in the Castle Lager Rugby Championship to see what depth we have and there will probably be more changes next week."