Honours were just about even at stumps on Friday, with the Aussies 2-54 in response to the Black Caps' first innings total of 202.
Steve Smith (24 not out) and Adam Voges (9 not out) saw the hosts through to the close of play after openers David Warner and Joe Burns fell victim to the swinging pink ball under lights.
Warner (1) was caught in the slips off the bowling of left-armer Trent Boult, who together with Tim Southee got plenty of movement in the night session, before Burns (14) chopped on off the bowling of Doug Bracewell.
Earlier, Australia's pacemen dominated throughout New Zealand's innings, bowling the tourists out for 202, but the success was soured by an injury suffered by spearhead Mitchell Starc.
The left-armer left the field toward the end of the second session and it was later revealed he had picked up a stress fracture in his foot, and won't bowl again in this match.
Before being injured Starc took three wickets - including the big scalps of Kane Williamson (22) and Black Caps captain Brendon McCullum (4) - on his way to bowling figures of 3-24.
Josh Hazlewood also took three wickets, while Siddle and Lyon took two each.
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