Needing to anchor the Black Caps' fourth-innings effort, New Zealand's best bat was caught at short leg from the first ball Nathan Lyon bowled on day four just before the main break.
Lyon had one pop out of the footmarks and into Williamson's gloves on 14, after Mitchell Starc had already had Jeet Raval edging to point for one.
Matthew Wade earlier wore several body blows on Sunday before falling for 17, as one of three Australians to be dismissed in the opening hour as they declared at 9-217.
It left the Black Caps needing to either survive more than five sessions against the pink ball to draw, or pull off the biggest run-chase in Test history to win.
The previous record was the West Indies' effort to hit 418 in the fourth-innings in 2003, but this appears a far more difficult pitch as the cracks begins to open.
Regardless, New Zealand will be spurred on by their short-ball barrage ahead of the next two Tests in Melbourne and Sydney.
Wade copped several balls from Neil Wagner (3-59) to his gloves and arm, as he almost led with his elbow at shorter balls from the left-armer.
He then eventually perished to a short ball, becoming the the fourth batsman out to a pull shot this innings.
Tim Southee took 5-69, as each of Australia's top six fell to shorter balls with a field of catchers set around the bat.
Joe Burns admitted it was tougher to deal with short balls from New Zealand's quicks who average around 130km/h, rather than those sent down at express pace.
"They have done it in the past and to all sorts of teams. We knew that tactic was coming," Burns said.
"It's tough because they are executing the balls they want to bowl.
"It's easier said than done to say you're just going to come around the wicket or for Wagner to bowl long periods of the short ball with that field."
Burns had hit a gritty 53 on Saturday as he and Marnus Labuschagne (50) provided almost half the runs in Australia's second innings.
