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New Zealand bowled out the hosts for 197 and then had a rain-adjusted chase changed to 182 - but couldn't even the series when regular wickets fell after the delay to see them bowled out 13 runs shy of victory.
The White Ferns had England in trouble at 118 for six when opener Lauren Winfield-Hill and Danni Wyatt were involved in a run out mix up that saw Winfield-Hill depart for 39.
Captain Sophie Devine later admitted the side lacked mongrel to finish off the England innings from there and they paid for it.
Wyatt made up for the run out mistake with 63 off 72 balls including a last wicket partnership of 52 with England number 11 Tash Farrant which carried the home side from 146 to 197 before they were bowled out in the 44th over.
Leigh Kasperek (3-31) and Hannah Rowe (3-41) led the way for the New Zealand bowlers.
New Zealand made a strong start in the chase at 61-1 and despite losing Suzie Bates (28) and Amy Satterthwaite (1), the White Ferns were still in a strong spot at 111 for four when rain stopped play after the 24th over.
If the rain had continued New Zealand had done enough to earn a victory via DLS but the fading sun was shining on England when the game re-started.
The readjusted DLS chase changed from 87 runs from 26 overs to 72 runs from 18, probably more favourable for England but still a manageable target with six wickets in hand.
However, Devine was bowled shortly after the restart by Nat Sciver for 28 and was followed by Katey Martin in the following over. Regular wickets continued when Hannah Rowe (7) and Brooke Halliday (29) departed and suddenly within 57 balls after the restart New Zealand's chase was in tatters.
England's fifth bowler Charlotte Dean finished with 4-36, taking all her wickets after the delay.
Devine said her side failed to back themselves and finish the England innings off, which proved costly.
"We're extremely disappointed, bowled England out for a sub-par total, we back ourselves to win those, rain-break or not, it was never run-rate pressure that would get us, it was wickets. You can't lose them in clumps against a strong English side," Devine said after the game.
"Got to go back to the drawing board, we tried too hard to get the lower order out. Have another crack on Tuesday. Got to have a bit of mongrel about us, winning is a habit and we haven't won much of late. Got to back ourselves, and tip it over the line."
The third game takes place on Wednesday morning NZT in Leicester.