The Australians dismissed the Black Caps for 317 with Kane Williamson the last man out for 140.
Australia's openers David Warner and Joe Burns then scored briskly to reach tea at 86 without loss off 14 overs.
Warner was on 47 and Burns was on 36.
Williamson's defiant innings ended when he was caught behind, giving Mitchell Starc his fourth wicket of the match.
He was congratulated by the Australian players as he left the field after his 178-ball knock speckled with 24 fours.
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The 25-year-old right-hander also became only the fourth Kiwi to score a Test hundred at the Gabba along with John Reid, Martin Crowe and Jacob Oram, with his 140 marking the second highest score by a New Zealander at the ground behind Crowe's 188.
Williamson played a lone hand for the Black Caps as wickets toppled around him on the third day.
Wicketkeeper BJ Watling added 67 runs for the sixth wicket with Williamson before he fell to the first ball of Mitchell Johnson's opening over of the day.
Mark Craig resisted for 46 minutes before he miscued spinner Nathan Lyon to Mitchell Marsh at point for 24 leaving Williamson at the crease on 86.
Doug Bracewell, dropped by Adam Voges on four, went on the fourth ball after lunch, bowled by Marsh for 16 to bring the injured Tim Southee to the crease.
Southee hit out lustily before he was bowled off-stump by Starc for 14 off as many balls.
Starc claimed the scalp of Williamson to finish with four for 57 and fellow left-arm paceman Johnson captured three for 105.