Virtually all that could go wrong did go wrong for the hosts at the Melbourne Cricket Ground, where injuries, yellow cards and skill errors hastened them to a 38-7 defeat and the loss of the Bledisloe Cup for a 21st successive year.
Jones will have to dig deep into the spare parts pile ahead of next Saturday's dead rubber against the All Blacks in Dunedin, where Australia face a hostile crowd and a shortage of props.
Both Australia's leading tightheads are injured, with Allan Alaalatoa to miss the World Cup after rupturing an Achilles tendon at the MCG, the team confirmed on Sunday.
Taniela Tupou also suffered a rib problem.
Queensland Reds prop Zane Nonggorr, who made his test debut off the bench in the 43-12 hiding by South Africa in Pretoria, has been recalled for Dunedin along with uncapped New South Wales prop Tom Lambert.
How Jones can shore up the Wallabies' leadership deficit and rebuild their confidence are different questions altogether.
Australia will be without co-captain Michael Hooper in Dunedin and possibly for the World Cup in September and October, depending on the severity of his calf injury.
Hooper's endurance and ability to run out the whole 80 minutes has been one of the rare shining lights through the Wallabies' gloomy World Cup cycle.
Those qualities were sorely missed on Saturday as the Wallabies collapsed in the final 20 minutes following the team's second yellow card in the second half.
Jones noted bluntly that his players had run out of gas and the yellow cards would hardly have helped.
The All Blacks scored four tries when the Wallabies were a man down and sealed the win with a three-try burst in seven minutes after Tupou was shown a yellow card in the 57th minute.
The Wallabies finished their winless Rugby Championship with five yellow cards from three matches, four more than the next-worst sides, Argentina and South Africa.
The All Blacks, disciplined as well as clinical, had none in the tournament.
Jones salvaged some positives from the MCG mauling, noting that Australia had the All Blacks on the back foot for the first 20 minutes and at the start of the second half.
However, the Wallabies repeatedly failed to turn pressure into points.
Rookie flyhalf Carter Gordon, starting his first match in the number 10 jersey, was culpable in that regard, having a forgettable night with the boot.
He and scrumhalf Tate McDermott, who relegated the experienced duo of Quade Cooper and Nic White to the bench, were comfortably outplayed by All Blacks counterparts Richie Mo'unga and Aaron Smith.
But Jones gave firm backing to the 22-year-old Gordon, calling him the country's best young number 10.
"Sometimes you have got to go through a bit of pain to bring young players through and I'm prepared to go through that," he said.
Jones's defence of his players would be heartening for them, and a contrast to the scathing reviews of fans on social media during and after the All Blacks game.
Yet he stopped short of backing them to convert Melbourne's meltdown into a Dunedin victory in a week's time.
"We're going to have work pretty hard, mate, aren't we?" he said.
"Dunedin's going to be fast but the opportunity's there."