Bernard Foley nailed a clutch 40m penalty with nine minutes to go to level the scores, and the Wallabies smothered an after-the-siren drop-goal attempt from Elton Jantjies to deny South Africa victory.
The result - just a fortnight after a 35-29 loss to the All Blacks in Dunedin - leaves the Wallabies with a draw and two losses ahead of next week's clash with Argentina in Canberra.
Western Force jerseys dominated the crowd at nib Stadium as fans protested against the axing of their beloved franchise.
The Wallabies' gold was scarce, with only about 15 per cent of the 17,528 crowd donning the national colours.
A chant of "Force, Force" went up before kickoff, and the fans chanted the name of their axed Super Rugby franchise at numerous other times in the game, as well as after the match.
Outside centre Jesse Kriel scored the first try in the 25th minute from a brilliant grubber kick and an ounce of luck.
Kriel dribbled the ball forward 25m and Wallabies flanker Michael Hooper and Springboks winger Raymond Rhule gave chase.
Hooper and Rhule collided just as they were about to reach the ball, with Kriel cruising in to pick up the crumbs and touch down in the corner.
However, the visitors' joy was short lived, with Israel Folau winning back the restart, and Beale producing a dodge-and-weave run to touch down.
An early head knock to hooker Polota-Nau gave 20-year-old Jordan Uelese an earlier-than-expected debut in the 18th minute.
Uelese made an early break, before Polota-Nau returned to the field after Kriel's try. Foley's penalty after the halftime siren gave the Wallabies a 13-10 edge at the break, and when Polota-Nau barged over after a lineout and rolling maul, the Wallabies led 20-10.
Hooper produced a try-saving tackle just metres from the line to stop Jan Serfontein's blistering run, but there was no stopping hooker Malcolm Marx, who barged over after a dominant rolling maul.
There was drama galore after the final siren as South Africa pushed for victory.
Even after Janties' drop-goal attempt was charged down, the Wallabies needed to produce some resolute defence to ensure South Africa didn't score a try.
They even had a chance to pinch it at the death after they forced a turnover, but a knock-on ended their hopes.
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