Sophie Devine and Maddy Green picked up a wicket apiece as well, but couldn't get the White Ferns off to a fast start when opening with the bat, with Devine making 25 from 22 balls before being stumped from some canny bowling from Georgia Wareham, while Green mustered just 10 from 17.
Suzie Bates' struggles continued with just three from eight balls, but Amy Satterthwaite (30 from 25) and Katey Martin (23 from 24) brought the hosts back to needing 30 runs from 30 balls.
However, they fell in quick succession, with Wareham, surprisingly only used for three overs, bowling Martin, and Satterthwaite dragging on to the similarly impressive Jess Jonassen (1-15 from four).
That left Kerr and Hayley Jensen needing 26 from 22 balls. The pair had been in this situation before, nearly seeing the White Ferns home from an improbable position against India at the Twenty20 World Cup earlier this year, and this time they went one better as Kerr broke the Ferns' drought.
The two teams resume their rivalry in the Rose Bowl – which New Zealand hasn't won since 1999 – on Saturday.