Australia declared their first innings before tea at an imposing 559 for nine, and shortly afterwards New Zealand lost the wicket of opener Martin Guptill.
Guptill was trapped leg-before by Mitchell Starc for just one run, with the New Zealand score on six.
They were 33 for one at tea with Kane Williamson on 17 and opener Tom Latham on 13, but still trailed the home side by 526 runs.
Australia, ahead 1-0 in the three-match series after a 208-run win at the Gabba in Brisbane, had resumed at 416 for two, with Warner on 244 and eyeing Matthew Hayden's record WACA score of 380 against Zimbabwe in 2003.
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However, he added just nine runs before some much-improved bowling from Boult had him edge the ball to Mark Craig.
It was the second-highest individual score at the WACA, behind only Hayden's massive knock against one of cricket's minnows.
Warner had helped Australia notch an opening day WACA record on Friday and posted the best Test haul in a single day by an Australian on home soil.
He also became the first batsman to score three Test centuries at the venue.
Australia captain Steve Smith had no such impact, making just 27 before he aimed a wild swing at Matt Henry (2-105) only to edge a catch to the wicketkeeper.
Paceman Doug Bracewell (2-81) provided a rare moment of delight for the visitors when he took a brilliant catch on his follow-through to remove Mitchell Marsh for 34.