The Wallabies suffered a setback even before the kick-off, with powerhouse prop Taniela Tupou ruled out after straining his hamstring during Friday's captain's run, replaced by uncapped Melbourne Rebel Jermaine Ainsley.
Jack Maddocks scored a consolation try for Australia after making his global debut from the bench but Naholo responded with two tries in two minutes to settle the issue.
Wallabies coach Michael Cheika has picked a new-look front row for Saturday's Bledisloe Cup opener, with hooker Tatafu Polota-Nau and loose-head prop Tom Robertson getting the nod for the all-important clash at ANZ Stadium. The 22-year-old they call the "Tongan Thor' has emerged as a significant contributor off the bench for the Wallabies". Now that bench unit has been compromised, with Ainsley facing a daunting task making his test debut against his country of birth.
Elsewhere, skipper Michael Hooper, Izack Rodda and Dane Haylett-Petty have shaken off injuries to take their place at lock and right wing respectively. Kurtley Beale 11. Marika Koroibete 10. Lukhan Tui 5. Adam Coleman 4.More news: Cardiff City vs Newcastle preview: It's Benitez vs Warnock
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They held on to prevent the Wallabies crossing the line in the first half, restricting them to penalties for Reece Hodge and Bernard Foley.
All Blacks captain Kieran Read admitted the Wallabies dominated the first half, with his team trailing 6-0 until Aaron Smith's opening try in the 39th minute.
To rub salt in a deep wound, sliced open by five second-half Kiwi tries, Israel Folau trudged up the tunnel late in the match with what appeared to be an ankle injury.
Subs: 16 Nathan Harris, 17 Karl Tu'inukuake, 18 Ofa Tuungafasi, 19 Scott Barrett, 20 Ardie Savea, 21 TJ Perenara, 22 Damian McKenzie, 23 Anton Lienert-Brown.