For the second match in a row Australia chased a target and were well on course to win as openers Mitch Marsh and Travis Head blazed the bowling to all parts.
But once they departed, it became much harder for the tourists as South Africa’s spinners put on the squeeze again, as they did in the 67-run win in the first match in Durban.
From overs 30 to 40, Australia managed 37 runs in Durban and just 35 on an excellent batting wicket in Johannesburg.
"It's certainly an area where we need to improve and we're well aware of that," captain Marsh said. "I thought we set up our innings really well in both games but we haven't been able to execute during those middle phases.
"It's a great learning curve, especially for some of our younger players. But you also have to give South Africa full credit for the way they've bowled during those periods."
Australia are on a fact-finding mission in South Africa, who host the 2027 Cricket World Cup with Namibia and Zimbabwe around this time next year.
Seeing the conditions first-hand could be a major advantage over other contenders for the title.
"I thought some of our younger guys performed really well. You see glimpses of what they're capable of and that makes the future exciting," Marsh said.
"Ultimately, though, we've been outplayed in this series, and we understand that.
"We just want to keep improving. We certainly don't want to be whitewashed, so we'll go to Potchefstroom (on Wednesday) determined to win that final game and play some good cricket."
