With their tails up, Bay of Islands started to dominate the game, and ten minutes into the second spell, sent Jim Anderson across the chalk to score a converted try.
Just ten minutes later, Jason Piheama backed the try up with one of his own.
Although the try went unconverted, Bay of Islands had a handy 19-3 lead, which was reduced quickly as Whangarei fought back in the last 15 minutes of the match, with an unconverted try by Hayden McCaw.
The visitors extended their lead with a penalty kick, before McCaw collected a welltimed offload and scored his second try of the game. First five Dan Wells added the extras, and with a few minutes left, both sides lifted their intensity.
Whangarei attacked Bay of Islands line, and their persistence paid off when Brent Murray stretched out to dot the ball in the closing minutes.
With a strong cross wind causing Wells some grief, he rushed the unsuccessful conversion, unable to get the two points which would have levelled the score.
A chuffed Bay of Islands manager Brent Hewitt said he and his team were stoked to win the shield back.
"What was best of all is we gave all the players a run. There is a lot of history with this shield, and we're happy to have it back in the Bay. The boys performed above expectations," Hewitt said.
While sub union rugby has slipped through the cracks in recent years, Northland Rugby Union are hoping to revive the Harding Shield and its significance, as well as using it as a development tool for young players throughout the region.
Next year, Hewitt said it is hoped there will be three rounds of the Shield next year, with games played early in the rugby season.