"The replacements made a big impact when they came on. The effort is still good and I am happy with the attitude of the players, but it is hard lessons we are learning as a team," said Coetzee.
South Africa scrapped to a narrow win at home over Argentina in their opening game of the Southern Hemisphere championship but then lost to the Pumas in Salta a fortnight ago.
They now head to Christchurch, where they will play New Zealand next Saturday.
Lock Lood de Jager, scrumhalf Faf de Klerk and fullback Johan Goosen are all doubtful after suffering injury on Saturday, the coach added.
Meanwhile, Wallaby skipper Stephen Moore has hailed the character of his side in snapping a six-match winless run.
It was a long way from the finished article but a buoyant, sometimes gritty performance they will hope to build the remainder of their Rugby Championship campaign around.
"There's been plenty of people outside the group giving their two bob on everything," Moore said.
"I'm just really proud the way that everyone's hung tight and worked hard and kept preparing as best they possibly can.
"The way we've stuck at it throughout the campaign is probably the most pleasing thing, when it's been tough."
Moore said the intense scrutiny of his own form had not bothered him in the lead-up to the match, which came on the back of two limp Bledisloe Cup defeats to New Zealand.
"I think it's part of the game, isn't it? Particularly in a leadership role, coach and captain, you're open to that and that's fine," he said.
"Everyone has their opinion. I've got no issue with that at all."
The only sour note was a possible knee injury to reserve prop Allan Alaalatoa, who was seen leaving the stadium in a knee brace and will have further scans on Sunday.
Alaalatoa helped swing the match Australia's way when he came on in the second half, at one stage even squaring up to giant Springboks lock Eben Eztebeth in an off-the-ball scuffle.
Team officials are confident it's not a major setback for the youngster, who was making his third Test appearance.
The Wallabies take on Argentina in Perth on Saturday in the Rugby Championship's fourth round.
