The key moment arrived in the 69th minute when the Wallabies set a 5m scrum.
There were none of the earlier wobbles of the scrum and 104-Test South African prop Tendai "Beast" Mtawarira went straight to ground under heat from Tupou.
Matt Toomua calmly potted the points for the 23-18 break, his fourth success from five shots and a key component in his man-of-the-match display to go with stout tackling.
The greasy, wet conditions made handling difficult and three handling errors by silky Boks fullback Willie le Roux explains errors by the Wallabies too.
Halfback Will Genia was mighty with his smart running, Kurtley Beale had moments but was largely hemmed in his new role at five-eighth and replacement Bernard Foley grabbed the intercept on full-time to repel a relentless South African rally.
Australian rugby need such guts and it was everywhere. Lock Rob Simmons made a game-day flight from Sydney where he withdrew from a Sydney Rays game to play as a sub after Coleman withdraw on the day for family reasons. Folau's ankle ruled him out hours earlier.
The precision of the Wallabies' fine try in the opening two minutes for Michael Hooper bore no resemblance to the power balance for the rest of the first half.
It was an 11-phase strike with Beale instantly into creative mode with a loop pass playing second receiver outside Matt Toomua.
What changed? The crunching power of the Springboks hurling bodies into rucks and their splintering, driving mauls off lineouts were a huge statement of their strength.
When Boks hooker Bongi Mbonambi was propelled over for 10-7 from one such surge there were serious danger signals for the men in gold.
The Wallaby forwards were never low enough to stall it.
It was not helped by experienced hooker Tatafu Polota-Nau looking completely spent after 20 minutes and lasting just 33. He had made a draining round trip to London to play for his English club Leicester last weekend so there was some excuse but it amplified the inexperience in the Wallabies pack.
Down 15-7, the Wallabies need a spark or a lucky break and they grabbed the later.
A completely misfired lineout throw from Mbonambi 5m from his own tryline flew so high and long it bounced straight into the arms of Toomua who slide over for a desperately needed try and 15-14.
It reignited the Wallabies and a towering 53m penalty goal on halftime from power-boot Reece Hodge made it 18-17 at the break.
The poor crowd of 27,849 was around 3000 under the corresponding Test in 2016 against the Boks and was a fair litmus test that the Wallabies' patchy form this season is costing them big money at the turnstiles as well.
The voices roared when the Wallabies went on the attack in the second half but two visits to within metres of the tryline were wasted, firstly by Rob Simmons knocking on a Will Genia pass and then Marika Koroibete pushing a pass that was intercepted.
Wasting such chances in the Boks' quarter were crushing because replacement hooker Folau Fainga'a was twice pinged for crooked throw-ins.
Several thumping tackles from Fainga'a and earning a key penalty made his impact invaluable.
The Wallabies got their huge lift when replacement prop Taniela Tupou ran on in the 47th minute because "Tongan Thor" instantly added venom to an inconsistent scrum.
