But the Hawks secured a vital bonus point which kept them on top of the standings and allowed them to claim the Gallaway Trophy.
Southern had to settle for second place and will play Taieri in one semifinal and Harbour meets University A in the other. Both games are at Forsyth Barr Stadium.
Taieri produced an impressive second half to dispatch Dunedin 46-8 and University A brushed aside Green Island 60-24.
Kaikorai had too much class in its backline for Pirates, winning 46-31, and Zingari Richmond beat Alhambra Union 34-17.
Southern 24
Harbour 22
Southern faced a dilemma with two minutes remaining at Bathgate Park. It could kick a penalty goal and probably secure the win, or roll the dice.
The Magpies trailed Harbour 22-21 and needed to win by eight points or more to knock the Hawks off the top of the standings and claim the Gallaway Trophy.
The home side opted for the shot and the reliable Bryce Hosie slotted it. But Harbour kept Southern pinned down for the remaining few minutes, and while Harbour lost the game, it secured pole position for the semifinals and won the Gallaway Trophy.
That looked a long way off at halftime, when Southern led 21-5. The Magpies enjoyed a large portion of possession and played the game mostly in the opposition half.
Hosie drilled two penalties. The first saw him reach 200 points for the season and he celebrated with a try, having got on the end of the chain following some wonderful lead up work by the team.
Powerful No 8 Mika Mafi set up a second before the break. He burst off the back of a 5m scrum, ran across the field and drew in the last defender before off loading to winger Josh Gordon.
Harbour's pack was more clinical in the second half and Southern's pack wilted just a little. Lock Ryan Thompson received a yellow card for a professional foul and moments later reserve halfback Vinnie Isherwood got across following a long assault.
Physical loose forward Naulia Dawai also scored following another siege, and Logan Allen's penalty put Harbour in front with about five minutes remaining.
Taieri 46
Dunedin 8
Taieri scored in the opening minutes through a charge down to prop Nick McLennan at Peter Johnstone Park.
But it was in the second half when the defending champion Eels showed their class, running away to win by nearly 40 points.
First five eighth Josh Casey brought up a significant milestone with a penalty 25 minutes into the game. He needed just two points to overhaul Daniel Soper's record season tally of 260, set for Dunedin in 1997.
Casey finished the match with 16 points, which means he has scored 275 points this season. He has at least one more game to add to his total and may yet get past 300 points if Taieri makes the final.
Dunedin had its best patch following the early try. It dominated for 20 minutes but could manage only a penalty.
Then openside flanker Grayson Kite show great pace to score from 30m out, giving Taieri a 15-3 lead at the break.
Michael Collins scored three second half tries to help the Eels pull away. He ran hard and straight and is looking sharp following a long injury layoff.
The win saw Taieri put two trophies back in the cabinet - the Fitzgerald Walker Cup and the Speight's Challenge Shield.
Lock Mark Grieve Dunn was outstanding for Dunedin and halfback Ed Hoadley had a strong game.
Kaikorai 46
Pirates 31
The return of experienced midfield back Jayden Spence gave stability to a Kaikorai backline prepared to attack from all parts of Hancock Park.
Spence, who has been sidelined by injury for much of the season, used his strength inside the 22m to score two of Kaikorai's seven tries.
He was backed up by counter attacking fullback Tony Ensor, who used his pace to score a first half try and create other scoring opportunities for the backs.
Flanker Theo Commissaris, the best Kaikorai forward, created Kaikorai's first two tries with breaks inside the 22m. He scored one himself in the second half after a 22m run.
He was backed up by hard working No8 Jared Goodson and blindside flanker Johnny Appleby.
Kaikorai scored five tries in the first half to lead 31-12 at the break and added two more tries in the second half.
Pirates had the better of the second spell through the driving play of prop Craig Millar and No8 Josh Clark, who also made seven clean lineout takes.
Three of Pirates' five tries came in the second half when they outscored Kaikorai 19-15. The best Pirates back was first five eighth George Wigley, who broke down the left flank for a 40m intercept try.
Zingari Richmond 34
Alhambra Union 17
Zingari Richmond celebrated stalwart Chris Bell's 200th premier game with a good win at the North Ground for the Grace Mills Trophy.
Bell had a solid game but it was midfield back Lachie Moore and fullback Christian Walker who were causing the majority of the problems. Neither scored but the pair opened up the defence a lot. Moore set up Shaun Driver for the game's first try when he carved through the midfield.
Loose forward Blair Tweed had an industrious game and scored two tries. Prop Stu Young also grabbed a try, which was good reward for a busy game.
For Alhambra Union, forward Ben Tuiomanufili showed surprising pace and was solid at No2 in the lineout, and prop Witana Petley held up his side of the scrum. Both scored tries in the second half for the home side.
Alhambra Union has made a habit of getting offside at the breakdown this season and it proved costly again.
With Pirates picking up a bonus point against Kaikorai, Alhambra Union slipped down the standings one spot and will play Green Island in the wooden spoon match.
The game was delayed for about 25 minutes while Alhambra Union prop Tristan Fuli, who injured his neck, received some medical attention and waited for an ambulance.
University A 60
Green Island 17
A slick backline operating off a strong set piece was too much for Green Island to handle, as University A racked up nine tries in a convincing win at Miller Park.
The students scored the opening 36 points. Their set piece provided a powerful platform to launch from, forcing Green Island on to the back foot and creating holes in the defensive line, which University A exploited well.
Green Island did not go down without a fight, however, scoring a try on halftime then nabbing two more after the break, taking the score to 36-17.
Green Island looked good in patches, playing a tight game and using forward runners to build multiple phases. There were too many mistakes, though, and some flimsy defence allowed University A to score four more tries to Green Island's one.
Matt Faddes and Liam Fitzsimons both looked dangerous in space for University A, showing pace and the ability to beat defenders in scoring two tries each.
First five eighth Fletcher Smith got the ball through his hands quickly to give his backs space, while the forwards were powerful as a unit.
Jackson Hemopo was strong for Green Island, providing go forward with ball in hand and running 50m to score a great try after cleaning up a loose pass from University A.
Alongside him, Nela Manu worked hard, while Sam Finau made a couple of good breaks.
