Kane Williamson, 45 not out at the close of play at Hagley Oval, appears the last hope for the hosts with Corey Anderson on nine and New Zealand still needing another 14 runs to make the visitors bat again.
"It's always a big wicket for us. He's played nicely," Australian batsman Adam Voges told reporters. "We bowled well to him at the start and it took him a while to get going.
"The plan is to try and keep him as dry as possible and limit his scoring options ... (but) we are certainly in a good position."
Australia, who were dismissed for 505 earlier on Monday for a 135-run lead, comprehensively won the first game of the two-match series in Wellington and only need to draw the second to seal the number one ranking in test cricket.
Pattinson, who had Martin Guptill out for a duck before tea, also dismissed Tom Latham (39) and Henry Nicholls (two) after it as clouds, strong winds and cooling temperatures gave the Australians the perfect conditions to swing the ball.
The 25-year-old had figures of 3-29 from 12 overs.
Josh Hazlewood grabbed the other wicket when the retiring Brendon McCullum was brilliantly caught by David Warner at short mid-wicket for 25, a ball after he had belted his 107th test six over square leg.
The 34-year-old McCullum, who scored the world's fastest test century from 54 balls in the first innings, was given a standing ovation back to the pavilion.
He ends his career having scored 6453 runs at an average of 38.64 with 12 centuries, 31 half centuries and a top score of 302, the only test triple century by a New Zealander.
Latham and Williamson had steered New Zealand to 43 for one in their second innings at tea after the hosts had finally dismissed Australia about an hour after lunch when they took five wickets.
The visitors had gone to lunch at 455 for five before Neil Wagner added the wickets of Voges (60) and Mitchell Marsh (18) to the two he took on Sunday.
Wagner then completed his second five-wicket haul when he had Peter Nevill caught by wicketkeeper BJ Watling for 13, and then Hazlewood caught at first slip by McCullum for the same score.
Wagner finished with career-best figures of 6-106.
"It was a pretty special bowling performance," Watling said. "I think it was about 25 overs of good fast short-pitched bowling. He's done it for us on many occasions and today he got his rewards."
(Editing by Peter Rutherford/Amlan Chakraborty)
