Leading 10-3 after 15 minutes, thanks to Scott Sio's first try at international level, the Wallabies were run down 18-10 by a gallant Springboks outfit that took its chances with the boot.

Five-eighth Morne Steyn kicked four penalties from five attempts as well as two crisp drop goals to help his side snap a three-game losing streak and keep South Africa's unbeaten record against Australia at Loftus Versfeld intact.

The Wallabies were in the contest until the final stages but were unable to capitalise on some favourable field position and more possession than their rivals.

"I felt we were right in the game the whole time if not in control of the game," Cheika said. "We played a little bit better than we did in Brisbane but we didn't capitalise on the moments we had. There were a few good performances but we lacked the consistent quality. We showed good patches of quality and then we weren't consistent with that.

"We had many visits down there, to their territory, and we didn't pick any points up from many of them. That just about sums it up really. [If] we take our points down there, we win the game. We worked quite well to get into situations down there ... we didn't get enough shape to score another two or three tries, which we really should have done."

Cheika did not want to buy into whether Israel Folau should have stayed on the field after a late hit on Springboks winger Bryan Habana in the 34th minute but said it was a significant moment in the match.

In the 10 minutes Folau was off the field, South Africa came back from 10-6 down to lead 12-10 thanks to a couple of penalties from Steyn.

"What's the point, there's no point saying anything about it, is there?" Cheika said. "He [Folau] turned his back. What do you do? There's nothing I can say about it that's going to change anything anyway. It doesn't help when you play with one less for 10 minutes, that does take its toll eventually."

Despite nailing a number of long-range kicks at training during the week, winger Reece Hodge missed three shots on goal. If he slotted all three, it could have been the difference between winning and losing.

Cheika and captain Stephen Moore shifted the blame though, saying Hodge's missed kicks didn't differentiate the two sides.

"That's the game, mate," Cheika said. "The first one he hit, he mishit it and it just went under the bar. The other two [were] a bit out on the angle. I think we had our 10th debutant tonight for the season and we've got a very young, new side, a lot of new players, and they'll learn from those experiences around how to prepare and practise better so that [on] game day we'll be on the money."

Moore added: "Reece's kicking for the line was superb, he was getting some real distance there. That was terrific."

Cheika praised the Wallabies front-row as well as the individual efforts of Michael Hooper, Sean McMahon and Will Genia while suggesting some scrum penalties late in the piece that went against Australia could have affected the outcome.

"They were pretty important [calls]," Cheika said. "They swayed the game pretty heavily, the field position of the game and the points scoring. Yeah, they were influential. We had a lot of ball down so that's good. We haven't had a lot of that this year so we got ourselves in position but we were penalised at key moments down there."

Moore backed up Cheika's belief the Wallabies were better than last time when the sides met in Brisbane in September and was confident the group would take positives from the 18-10 defeat into their next match against Argentina in London next weekend.

"It's a constant journey, we haven't spoke about revivals or anything like that we just want to keep improving and like Cheik said we played better than Brisbane tonight but we didn't get the win," Moore said. "The rest of our games are away from home so you've got to get up quickly and go back again."