Ahead by 14 points at the break, Otago never fired a shot in the second stanza, as Harbour, riding on the back of a favourable penalty count, ended up a convincing winner.
The loss, the fourth in a row, leaves any chance of making the all-important top seven at the end of the season a forlorn hope.
Otago will stay at the bottom of the ITM Cup for at least another week, and realistically must win all the rest of its games to get into the top seven.
Otago did not score a point in the second period, while Harbour got 26, and was running on as the game ended.
The visiting side was looking comfortable at the break, up 23-9, and started the second half well, but could not get over the tryline.
And then its game fell apart, with too many knock-ons, poor options and indiscipline.
Worryingly, its energy levels went down the further the game went on.
Referee Bryce Lawrence penalised Otago by more than two to one in the match, so Otago just could not get out of its half.
Harbour sealed the win in the dying stages when Otago winger Fetu'u Vainikolo, trying to run from his line, threw a wayward pass and it was picked up by Harbour flanker Malakai Ravulo, who cantered over to score his second try.
Otago coach Phil Mooney was at a loss to explain what unfolded in the second half.
"I do not know what happened.
Things we spoke about doing we just went away from," he said.
"You saw the best of it and the worst of it over 80 minutes.
It was very disappointing.
"We spoke at halftime about specific things we wanted to do and we started well for the first five minutes.
"But then we started drifting away and I and David [assistant coach David Latta] can't explain it."
The first 20 minutes of the match rather meandered along and neither side could keep its hands on the ball for a long enough period.
The ball was being turned over too often from both the teams, and two penalties apiece by Glenn Dickson and Ben Botica was the best the teams could manage.
But Otago, in its first sustained attack, got the first five pointer after 22 minutes, with replacement prop Halani Aulika getting across the line.
Otago nudged it towards the line through a series of phases.
Then Aulika, who looked strong on the break, burst out of a ruck to the home team's surprise and could not be stopped by the back-pedalling defence.
That try was followed by another score straight from the kick-off.
The ball bounced up to centre Ben Smith and he put the pedal down.
When blocked 35m out, he cleverly kicked ahead and winger Joe Hill showed his pace to be the quickest to the ball.
All of a sudden, Otago was 14 points up, and although Harbour came back well, the visitor managed to keep its line intact for the rest of the half.
Botica nudged over a penalty three minutes from the break, but Dickson immediately replied with a penalty in the last act of the first period.
Otago had little territory or possession in the first half, but its defence was sound, while North Harbour showed poor ball security.
But the first half became a distant memory for Otago as it imploded after halftime.
No 8 Adam Thomson tried hard for Otago, and lock Hoani Matenga got through plenty of work.
Smith set up the try well, and fullback Chris Small did little wrong, and was wrongly called at a critical time for kicking the ball outside the 22m line.
The scrums were, as usual, a mess, although worrying for Otago, prop Sam Hibbard and hooker Liam Coltman both left the field with shoulder injuries.
