England, who lost Saturday's opening Test 29-10 following a late collapse, had looked to have snatched the win when Katy McLean slotted over her third penalty of the match with two minutes to go to put Gary Street's side 9-7 ahead.
However, New Zealand mounted one late bid for victory and were rewarded when full-back Selica Winiata crossed right at the death for a converted try which sealed the match and the series for the Black Ferns.
Earlier, two McLean penalties had given a much-changed England side a 6-0 lead at the break despite the tourists being a player down for a spell after lock Joanne McGilchrist was sent to the sinbin.
England held that advantage until the 70th minute when world champions New Zealand turned things round with a try from Winiata, which was converted by Kelly Brazier.
England battled back to reclaim the lead through McLean's late penalty, but they then saw victory agonisingly snatched from their grasp right at the end through Winiata's superb try.
The third and final Test will be played in Pukekohe on Saturday.