The Wallabies entered Saturday night's (Sunday morning AEST) Rugby Championship match looking to win back-to-back Tests against the Springboks in South Africa for the first time since 1963 following last week's famous 38-22 triumph in Johannesburg.
South Africa led 20-7 approaching halftime, but the Wallabies hit back hard after the break and closed the margin to one point in the 68th minute when reserve hooker Brandon Paenga-Amosa touched down following a successful rolling maul.
O'Connor slightly slipped during his conversion attempt, pulling the kick to the near side in what proved to be a major missed opportunity.
South Africa extended their lead 30-22 in the 75th minute, but O'Connor had a chance to close the gap back to five points three minutes later with a 25m penalty from a slight angle.
O'Connor pushed that kick to the right this time, and his 50m penalty attempt in the 80th minute - which would have at least given Australia a losing bonus point - fell short.
Yet despite not coming away with the win, it was another brave and encouraging performance from the Wallabies, who were again hamstrung by more injuries.
A devastated Tom Wright lasted just four minutes before going off with a left knee injury, while scrumhalf Nic White was forced off in the 13th minute with concussion after his head was slammed into the turf during a slinging tackle.
Prop Taniela Tupou dislocated his left pinky shortly before half-time, and outside centre Joseph-Aukuso Suaalii was subbed out at the break with an apparent head knock.
It came on top of the Wallabies losing skipper Harry Wilson (knee), James Slipper (concussion) and Dylan Pietsch (broken jaw) last week.
"I'm super proud of my boys," stand-in Wallabies skipper Fraser McReight told Stan.
"We lost a few good men out there, and under a bit of adversity we fought right until the end.
"Tonight could have gone either way. We will lick our wounds and come back for Argentina."
South Africa scored two penalties inside the opening six minutes of the match before the Wallabies struck back through debutant Corey Toole in the eighth minute..
White was the mastermind behind the try, with his quick tap-and-go and subsequent dribble kick allowing Toole to run on to the bouncing ball.
South Africa replied soon after, with Handre Pollard's cross-kick finding an open Canan Moodie for an easy try.
Stand-in Wallabies captain Fraser McReight was denied a 13th-minute try due to an earlier knock-on, and Australia were left to rue twice turning down kickable penalties in favour of going for touch.
South Africa's defence held firm on each occasion, and the scoreline read 20-7 when forward Kwagga Smith barged over in the 35th minute.
O'Connor's penalty after the half-time siren reduced the deficit to 10 points at the break.
Australia struck first in the second half when O'Connor's chaos kick couldn't be controlled by Springboks winger Moodie, allowing Max Jorgensen to swoop on the loose ball and race over.
A Wallabies win in Cape Town for the first time in 33 years was well and truly on the cards when Paenga-Amosa scored with 12 minutes remaining, but O'Connor's conversion miss proved to be a huge turning point.
One of the many positives to come out of the match for Australia was the debut of Toole, whose extreme pace and no-fear attack on the ball was a constant threat throughout the night.
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