Within 10 minutes of the restart, the scores were level at 24-24. Brad Armstong scored minutes into the second half with Angus McDonald also going over.
MacDonald put the Bay in front after a penalty from out wide had hit the posts, only for Harbour to infringe as they tried to recover the ball, giving MacDonald a much easier second chance.
The game then see-sawed, with Harbour hitting back with a try out wide to retake the lead with 10 minutes to go.
The Bay's Alex Pohla scored to restore his side's advantage, MacDonald converting from out wide to make it 34-31, and in the final minute Leethan Rawiri added the icing to the cake in the final minute, making it 39-31.
The win sets up a Battle of the Bays clash with Hawkes Bay on Sunday.