They bagged their first try in only the third minute when second-five Charlie Ngatai busted through to put halfback TJ Perenara across the stripe but they had to wait nearly 20 minutes for their next when first-five Lima Sopoaga danced through the defence.
Sopoaga then turned provider as he dished off a nice pass to Ngatai who waltzed through a woeful would-be tackler as Wellington shot to a 21-0 lead.
But, Wellington's poor lineout and mixed handling hindered their ability to put Harbour away and the visitors finally got on the board five minutes from half-time as replacement back Nafi Tuitavake finished off a scintillating Francis Saili burst.
Then before the Wellington players had barely caught their breath it would have been taken away by the dazzling footwork of 18-year-old Harbour wing Tevita Li who cut through four tackles to score on the stroke of half-time.
Another Codey Rei conversion gave the scoreboard a bizarre 21-14 look in favour of Wellington, who should have held a much bigger lead after the opening 40 minutes.
Rei then brought Harbour within four mid-way through the second spell as he added a penalty but when Ngatai completed his double it gave Wellington a decent 12-point.
Following a couple of penalties from both sides, Wellington's Eric Sione was sent to the sin bin and Saili scored under the sticks as Harbour crept in to the contest with only a few minutes left.
Wellington managed to hold on but they simply never clicked and probably suffered from making so many personnel changes from the team who beat Taranaki in round two.
A woeful home crowd of 2306 braved the biting wind at Westpac Stadium, while Wellington's players wore their club socks as part of a tribute to their heritage, which made for some eye-catching colour combinations.
Try of the match: Tevita Li is only 18 but keep an eye on this kid. The Harbour wing showed some magical footwork to beat four players on his way to an exciting first-half try.
Star turn: North Harbour centre Francis Saili was a danger with ball in hand throughout this one as he proved tricky to put down. He scored a fine try and laid on another in an impressive outing.
Wellington 35 (Charlie Ngatai 2, TJ Perenara, Lima Sopoaga tries; Sopoaga 3 con, 3 pen) North Harbour 27 (Nafi Tuitavake, Tevita Li, Francis Saili tries; Codey Rei 3 con, 2 pen) HT: 21-14