The Kangaroos recorded their third straight win over the Kiwis this year thanks to a 10-point haul from Jonathan Thurston.
Thurston collected a try, a conversion and two late penalty goals to get the green and gold home.
Some brilliance from his opposite half in the dieing stages almost stole the game for the Kiwis.
Blake Ferguson crossed in the first half before he set up Thurston for his try.
Australia were in control at half-time with a 10-0 lead.
New Zealand came back into the match when Solomone Kata crashed over from dummy half.
Thurston slotted two late penalties, putting the Kangaroos 14-4 in front.
But in the final 10 minutes Johnson set up Jordan Rapana in the corner with a brilliant chip and chase.
Johnson was then held up over the try-line right on full-time, with the video referee ruling no try.