The Springboks forwards dominated New Zealand in Dunedin on September 15, but their effort was wasted by some woeful profligacy with the boot as 20 points went begging in the 21-11 loss.
"We've worked hard the last few weeks and the front row gave one of their best performances and the loose forwards got stuck in as well," Van Graan said on Tuesday.
"We can improve on the lineout, where we lost a couple of balls, but the kick-offs were good and so was the ball retention - we had our lowest turnover rate of the whole year.
"I'm really proud of the performance against the All Blacks, we played some of our best rugby and to have 58 percent territory and 52 percent possession against them at home is a great effort.
"Unfortunately, we just didn't get the points."
However, Van Graan warned that the Nathan Sharpe-led Wallabies would provide another major challenge to his forwards, much as Australia did when they beat the Springboks 26-19 in Perth on September 8.
"Australia scrummed very well against us and Nathan Sharpe is one of the best locks of all time, so their lineout is tricky and they kick to different places to put you under pressure," the assistant coach added.
"Playing against the number two side in the world is always a massive challenge."
Experienced tighthead prop Jannie du Plessis said that while New Zealand were a daunting physical prospect in the scrums, the Wallabies relied more on intelligence and strategy.
"The All Blacks view scrums in the same way we do, as a place to exert physical dominance over the opposition. The Wallabies are much more tactical, they know what they want from certain areas of the field," he said.
"So it's a big challenge against them, they have a great loosehead in Benn Robinson and he scrums well with Tatafu Polota-Nau, they're both short and stocky."
Du Plessis played down the youthful nature of the Springboks pack in Dunedin, in which only he and fellow prop Tendai Mtawarira have more than 30 caps, saying that the inexperience helped create a never-say-die attitude.
"There are some advantages to inexperience, because those players are hungry and will play better than someone who has played a hundred tests and has a 'been there, done that' approach. As they say, 'a hungry dog hunts best'," he said.
Van Graan said it was important the Springboks showed an improvement in Pretoria and took another step forward in their progress.
"You can always improve and evolve and we started with the base, it's about finding your feet at this level," he said
"But we've grown a lot, there's been a lot of progression, our ball-retention and contesting on the ground is much better.
"You evolve step-by-step and we hope we take another step on Saturday. Hopefully, we can go from a good performance to a great winning performance," Van Graan added.
The assistant coach also highlighted the need for better defence against the attack-minded Australians.
"The Wallabies are a big threat, especially with their reverse attacking lines, Digby Ioane and Dom Shipperley in particular. We will have to improve our defence and hope our kicking game is spot on."
South Africa will name their team on Wednesday.