The two batsmen who made it Australia's day, opener Joe Burns and captain Steve Smith, were dismissed in near identical fashion shortly before the end.
Both players pulled short balls from Wagner and were caught at backward square leg by Martin Guptill. Had it not been for Wagner's spirited late burst, New Zealand would likely be significantly in arrears going into the third day.
Burns and Smith added an Australian record 289 for the third wicket against New Zealand, eclipsing the old mark of Ian and Greg Chappell, 264, set at Wellington in 1974.
Until the late Wagner play, New Zealand's only success had come in the fourth over of the day, when in-form lefthander Usman Khawaja was caught by McCullum at first slip off Trent Boult.
After that it was the Burns and Smith show as, by blending watchful defence with assertive shotmaking, they appeared to be shutting the door on New Zealand's aspirations of levelling the series.
Burns completed his third test hundred, his highest score, 170, and second against New Zealand, this summer, while Smith compiled his 14th century, 138.
Smith had one major scare in the over before tea when he was clunked a fierce blow on the back of his helmet by a lifter from Wagner.
Smith slumped to the ground and needed a couple of minutes to recover in a scene reminiscent of the tragic Phil Hughes incident, from which the Australian batsman died in late 2014.
Burns, too, had a worrying moment of a different sort, on 35, when he was given out caught behind off seamer Matt Henry. He immediately signaled for a referral and replays showed the ball brushing his sleeve.
His was a grafting innings, and he batted 440 minutes, faced 321 balls and hit 20 fours. Smith was in the middle 352 minutes, faced 241 balls and hit 17 fours.
Neither batsman gave a chance in their innings', but too much of the bowling was pedestrian and too often the bowlers were unable to keep the heat on the pair.
New Zealand tried a variety of tactics, with field settings and bowling strategies but to no avail.
They had opted for an all seam attack for this test, dropping specialist offspinner Mark Craig.
It was not an unreasonable call, as Craig has been hammered by Australia this summer and there were hopes a green pitch would give continued seam assistance.
But it's left them short in the spin cupboard with only the occasional offies of Kane Williamson for relief.
Until Wagner struck, it had been a depressing day of toil for little reward. Wagner lifted the spirits and kept New Zealand afloat in the match.
He finished with two for 63 while Boult has two for 85.
SCOREBOARD
WAGONWHEEL
MANHATTAN
