Captain Ross Taylor and Dean Brownlie strove hard to keep the innings afloat against demanding seam bowling from Peter Siddle and James Pattinson.
Taylor, dropped the previous day on 14, had a second life at 48 when Pattinson spilled a sharp return catch, eventually edged to first slip; Brownlie, after a painful blow on the left wrist, couldn't avoid a good delivery and followed Taylor back.
The lower order decided on a policy of hitting out, and new cap Trent Boult clouted three fours in successive balls from Siddle before the end.
By the time of the 12th over of Australia's innings, New Zealand were on their third new ball, the ongoing issue of balls being knocked out of shape during this series continuing.
Warner was aggressive, and drove hard; Hughes was more circumspect. Both had their luck, especially Hughes who was given not out to a legside catch in the third over by Chris Martin before he had scored.
New Zealand decided not to seek an umpires review, and it proved costly, the ball showing up as having brushed Hughes' glove on the Hot Spot replay.
New Zealand needed early success, but were unsure so decided to keep their decision review system options open for later in the innings - teams are limited to two unsuccessful appeals per innings before the ability to refer a decision upstairs is removed.
Warner has reached 47 from 50 balls, while Hughes will start the fourth day on 20.
The upshot is that New Zealand must hope the pitch begins to deteriorate from the start of day four, as it's expected to.
Already the occasional ball is keeping low, but New Zealand do not have a top class spin option, with allrounder Dan Vettori ruled out of the test through a hamstring strain.
New Zealand are after their first win in Australia since 1985, and just their third on Australian soil in 28 matches
