The result leaves the hosts 2-1 in front ahead of the fourth and penultimate test in Auckland on Wednesday.
Japan, who won the opening match of the series, were the first to strike when Shiho Otsuka scored from a field goal in just the 10th minute.
But the New Zealanders did not take long to counter attack, with Anita Punt driving the ball up the middle of the field and passing to birthday girl Katie Glynn, who met the Japanese goalkeeper for a one-on-one battle, which resulted in Punt picking up the loose ball and capitalising on the open goal.
The momentum continued for the home side as Glynn then flicked the ball between the goalkeeper's legs off a penalty corner variation to give New Zealand a 2-1 advantage at halftime.
The Japanese refused to go away though and they drew level early after the restart when Akane Shibata scored.
But again New Zealand hit the lead, this time via Stacey Michelsen, who took the ball into the circle before firing a strong shot into the far corner of the goal to mark her 50th test appearance in style.
They almost immediately doubled their lead when Charlotte Harrison scored off a reverse stick shot which went into the bottom corner of the goal before Japan had the last say Misato Katamine scoring barely one minute after Harrison.
Result:-
New Zealand 4 (Anita Punt, Katie Glynn, Stacey Michelsen, Charlotte Harrison) Japan 3 (Shiho Otsuka, Akane Shibata, Misato Katamine). Halftime: 2-1.
