The hosts grabbed a 1-0 lead in the three-Test series, when they rolled the Black Caps for 317 in the morning session on day five at the Gabba.
McCullum was incorrectly given out on 80 by umpire Nigel Long, replays confirming the ball deflected off the pad before flying to Steve Smith in the slips.
McCullum, renowned for being courteous on and off the field, failed to hide his frustration.
The 34-year-old punched the air then stormed off the field, unable to challenge the call as NZ had used their two reviews.
“It was a bad decision,” former Australia skipper Mark Taylor observed on the Nine Network.
“But I don’t have a lot of sympathy for Brendon McCullum and the players when they keep using them up frivolously.”
NZ resumed at 3-142 on Monday, their pursuit of 504 stumbling in the fifth over of the day when Ross Taylor was out in front of a threadbare crowd.
The seven wickets to fall were shared by Mitch Marsh, Josh Hazlewood, Nathan Lyon, Mitchell Johnson and Mitchell Starc.
Johnson moved his career tally to 310 Test wickets, meaning the left-armer is now equal fourth on Australia’s all-time list alongside Brett Lee.
McCullum departed in the 79th over – some nine balls later the review count was reset.
It was an unfitting end to an entertaining knock from McCullum, who resumed on four and had no interest in shelving his hard-hitting ways.
The veteran took 44 balls to race past 50, bringing up his half-century with a six back over the head of Nathan Lyon.
McCullum also slashed deliveries from Starc and Johnson to the fence with exquisite timing and pulled the majority of short balls sent down by the hosts.
The exception was in the 75th over, when he charged allrounder Marsh but was struck on the helmet.
It was a glancing blow, and McCullum got on with things with minimal fuss until he was dismissed by Marsh.
“I probably got a bit lucky with that one,” Marsh quipped.
Marsh then trapped Doug Bracewell lbw with his next delivery but Tim Southee survived the hat-trick ball.
It only delayed the inevitable.
Hazlewood was handed the second new ball and struck with his second delivery, Southee caught behind.
Southee reviewed the dismissal and looked unhappy when he wasn’t successful – third umpire S Ravi sticking with the original decision due to inconclusive evidence.
Mark Craig and Trent Boult put on a freewheeling final-wicket partnership of 46 runs, frustrating the hosts.
The innings ended in the 89th over when Boult was out caught behind.
It was the most overs New Zealand have batted in the fourth innings of a Test in Australia.
But that will be scant consolation for McCullum, who faces a major challenge as he attempts to rebuild the side’s confidence before the second Test starts in Perth.
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