Pirates started full of promise and dominated the forward exchanges in the first four minutes but then a stray pass was quickly turned into points by Harbour, through a try to openside flanker Jason Kelly.
Harbour touched down again almost straight from the kick-off through centre Siaosi Folau to secure a 12-0 advantage after just seven minutes.
The game then settled down with neither side gaining any superiority until the 37th minute when Kelly was on hand again to snatch the ball from the back of a ruck and dive over for his second try and allow Harbour to go to the break with its tail up at 17-0.
A try to promising 18-year-old winger Marshall Suckling just 50 seconds into the half was just the tonic Pirates needed to get back into the game.
But Harbour was quick to regroup and, after a series of attacks, the ball went wide and with a two-man overlap found left wing Joel d'Sousa, who scored in the corner.
Kelly and No 8 Rawhiri Tapiati stood out for Harbour, while midfield backs Folau and Corey Kara had strong games.
Suckling was the star for Pirates.
Kearney was an inspirational leader from No 8, while blindside flanker Josh Clark and lock Wirimu Ruru excelled in all facets of play.
Harbour 25 (Jason Kelly 2, Siaosi Folau, Joel d'Sousa tries; Dan Snee conversion, Johnny Hughes penalty goal), Pirates 19 (Warren Kearney 2, Marshall Suckling tries; Glenn Dickson 2 conversions).
Half-time: Harbour 17-0.
Referee: Dave Kennedy.
