It took a moment of class from standout Sofeni Vakaniu to cut the defence to shreds. The silky centre drifted outside his marker and on to a beautifully placed pass to put fullback Dylan Chesney over untouched in the left-hand corner.
The conversion fell short, but it was not long before Harbour hit the front through a 70-metre solo effort from Vakaniu.
A clearing kick gone wrong went right - resulting in a defensive bomb that the Bay let bounce.
Vakaniu hit it at top speed and never looked back, making no contest of the race to the northern end of Murray Salt Stadium. That score made it 10-7 to Harbour at the break, which extended to 15-7 when slick hands from Harbour sent replacement Troy Brophy over in the corner.
A runaway try against the run of play from winger Jack McManaway and the resulting conversion from national junior touch representative Jordan Tuakana-Hudson reduced the lead to a single point, before Chesney added a second to make it 20-14.
The Bay had their chances down the stretch but could not manage to beat the scrambling defence, with Harbour holding for a well-earned victory.
Auckland East beat Waikato in the final 29-14, with Auckland West sneaking past Northland to finish third.
Counties Manukau won the play-off against King Country for seventh, leaving Thames Valley in ninth spot.
North Harbour 20 (Dylan Chesney 2, Sofeni Vakaniu, Troy Brophy tries)
Bay of Plenty 14 (Nikki Jacobs, Jack McManaway; Jordan Tuakana-Hudson 2 cons).