Nicola Carey (1-24) was preferred to Ellyse Perry (1-8) to bowl the final six balls, and was hit for four straight away, leaving a target of five runs from four balls for victory.
But Carey held her nerve, bowling two dots, and giving up just three singles, meaning the Kiwis needed three runs from the final ball to level the series.
Carey bowled it full, Green got an edge and it ran between the keeper and short fine leg, all the way to the boundary for a special victory.
"I'd back our bowlers to defend 21 off 12 ... but when you need three off the last four balls it can go either way," Aussie opener Beth Mooney said after the match.
Mooney was the only Aussie batter to get going, notching 61 not out from 54 balls.
After the early loss of Hayley Jensen (3) and Amy Satterthwaite (6), Kerr and Frankie Mackay (46) added 54 runs for the third wicket to get the Ferns' run chase back on track.
Satterthwaite replaced Sophie Devine as captain, after the all-rounder was ruled out of the match due to illness only hours before the match.
Mackay's departure in the 12th over, caught at backward point by Mooney off the bowling of Darcie Brown (1-26), started the rot — with Katey Martin (5), Brooke Halliday (1) and Kerr all falling for a combined 20 runs.
"It's been a bit of a rollercoaster with the adrenaline rush right at the end," said Satterthwaite.
"I'm very proud of how everyone stepped up and performed their roles after Sophie was ruled out. Everyone snapped straight into game mode once we found out she wouldn't play and just got on with it."
Satterthwaite said a recent run of poor results — including a six-wicket defeat in the first match in Hamilton — had spurred the team.
"We have been building nicely and the belief in what we are doing was getting bigger, especially after Hamilton. That last game gave us confidence and we've taken a big step forward from the England series. I couldn't have asked for any more."
The series will now go to Eden Park in Auckland for the deciding game on Friday. - with news.com.au
Here's how the action unfolded: