The students ended with 59 points and were followed by Alhambra-Union 44, Pirates 43, Kaikorai 42 and Taieri 38.
In Saturday's semifinals, University A plays Kaikorai and Alhambra-Union faces Pirates.
Taieri was the unlucky team after giving a plucky display before losing to Alhambra-Union 16-12 in front of a supportive crowd at Peter Johnstone Park.
Southern and Pirates drew 34-34 at Hancock Park, with Pirates first five-eighth Glenn Dickson scoring 24 points.
Both teams gained a bonus point and the three points to Pirates were enough to clinch a semifinal berth.
Kaikorai gained a bonus point in the last few minutes to gain five competition points with a 32-14 win over Green Island at Bishopscourt.
Cam Rutherford, the first five-eighth, kicked 12 points for Kaikorai to pass 100 points for the season.
Dickson and Lewis Hancock (Southern) also reached 100 points on Saturday.
Matt Faddes, who was playing in the Highlanders First XV competition for South Otago High School last year, has been the find of the season.
His two late tries gave University A a 26-20 win over Dunedin.
Alhambra-Union 16 Taieri 12
Alhambra-Union survived a strong second-half rally by Taieri to claim a narrow win at Peter Johnstone Park.
The fleet-footed Alhambra-Union backline had control in the first half and led 13-3 at the break.
The only try came after 15 minutes, when Alhambra-Union won a scrum and spread the ball wide after two phases and winger Tilitili Puloka scored in the corner.
Alhambra-Union had come close to scoring on two other occasions and looked ready to blow the game apart in the second spell.
The Taieri pack had looked sluggish in the first spell, but it came out firing in the second spell, with loose forwards Charlie O'Connell and Jeremy Corliss being prominent.
Lock Matt Davidson and O'Connell provided clean lineout ball the pack used to drive downfield.
The Taieri revival started after two minutes when Tom Davie burst through the defence for 60m on a counter-attack that took play deep into the Alhambra-Union 22m.
First five-eighth Andrew Reid kept on the pressure with accurate kicks to the corners that kept Alhambra-Union on the back foot.
When he landed his fourth penalty goal from five attempts after 28 minutes the gap was reduced to four points.
The strong midfield defence of Luke Reihana and Paula Kinikinilau and sound covering by fullback Peter Breen shut the Taieri backline down.
The best Alhambra-Union forwards were No 8 Regan Turoa, with his ability to break the advantage line, and flanker Wahari Waitohi who was effective at the breakdown.
Lock Mitch Ewen made seven clean takes in the lineout.
Alhambra-Union 16 (Tilitili Puloka try; Luke Reihana 3 pen, con), Taieri 12 (Andrew Reid 4 pen).
Halftime: Alhambra-Union 13-3.
Referee: Ross Barnett.
University A 26 Dunedin 20
Promising fullback Matt Faddes was in superb touch and scored two late tries as University A came from behind to beat Dunedin at Kettle Park.
Dunedin led 20-14 and was in control when Faddes turned the game around with two brilliant individual tries.
He shot through a hole midway through the second spell and ran around the wing and fullback to score wide out to make it a one-point game.
Then, in the final minute, Faddes shot down the blindside and eluded the defence to win the game for the students.
It was a Houdini act by Faddes to take the game from a Dunedin team that had controlled possession and territory for the middle 40 minutes with its strong scrum and the powerful work of loose forwards Tim Fraser and Anthony Diack who dominated the breakdown.
The students had been in control in the first quarter and led 6-0 after first five-eighth Tom Halse kicked two of his three first half penalty goals after 14 and 18 minutes.
Dunedin took the lead 7-6 when midfield back Michael Walding used his strength to score the first try and Fraser added a second try after a rolling maul to give Dunedin a 12-6 lead.
A long-range penalty goal by Halse closed the gap to three points at the break.
Hooker Will Henry was dominant as the Dunedin pack continued to take charge in the second spell and extended the lead to 17-9 after Diack scored an intercept try.
The students came back into the game after 15 minutes, with lock Alby Herron winning two-handed lineout ball that was used efficiently by halfback Sean Romans.
Ryan Grant looked dangerous in the midfield.
The gap was closed to three points, 17-14, when Halse kicked in rugby league style for wing David Thompson to gather and crash over.
University A 26 (Matt Faddes 2, David Thompson tries; Tom Halse 3 pen, Ryan Grant con), Dunedin 20 (Michael Walding, Tim Fraser, Anthony Diack tries; Robbie Smith pen, con).
Halftime: Dunedin 12-9.
Referee: Tim Baker.
Southern 34 Pirates 34
Pirates could not quite win the Jack Hore Trophy for the first time since 2002, but a draw with Southern at Hancock Park was enough to lock away the Challenge Shield for the summer.
The end result was perhaps a fair reflection on the erratic but, at times, brilliant display put on by both sides.
Glenn Dickson scored 24 points, including two tries, and was masterful when directing play from first five-eighth.
His touch-finders and high-ball options inspired the forward pack, with flanker Josh Clark and lock Steve Mison quick to capitalise on Southern mistakes.
Prop Daniel Johnson, playing his 150th game for Pirates, was also a standout at the breakdown and helped to provide an edge over Southern in the scrums.
Halfback Steve Bruce proved a handful around the fringes and his quick thinking led to two of Pirates' four tries.
Southern halfback Lewis Hancock was also lively and provided Southern with an ideal platform on with to launch its attacks.
The Southern loose forward trio kept pressuring the Pirates backline into mistakes, while lock James Stevenson and frontrowers Ean Griffiths and Warren Moffat stood out in the tight.
Griffiths snatched a crucial tighthead with Pirates hot on attack with time almost up.
Southern 34 (Luke Herden 2, Lewis Hancock, Greg Zampach, Carl Anderson tries; Hancock pen, 3 con), Pirates 34 (Glenn Dickson 2, Josh Clark, Steve Mison tries; Dickson 2 pen, 4 con).
Halftime: Southern 22-21.
Referee: Todd Pullar.
Harbour 69 Zingari-Richmond 19
Harbour won the Bandy Scoles Memorial Trophy for the 34th time when it beat Zingari-Richmond at Montecillo.
Harbour dominated the game in all phases and was able to penetrate the flimsy Zingari-Richmond defence to score 11 tries in a sparkling display of attacking rugby.
The first try was scored by wing George Folau after just 90 seconds and the game was sealed after 15 minutes when Harbour had scored three tries and led 19-0.
Harbour scored seven tries in the first spell to lead 43-12 at the break and added four more in the second spell.
Folau displayed power and strength and centre Wayne Gibson was unstoppable with the ball in hand.
Flanker Eben Joubert also scored two tries and impressed with his strength and speed at the breakdown that produced numerous turnovers.
Ryan Olsen and Pete Mirrielees were strong in the front row.
No 8 Chris Bell and prop Jeremy Bekhuis were the only Zingari players to come out of the game with credit.
Harbour 69 (George Folau 2, Wayne Gibson 2, Enoka Tauafua 2, Eben Joubert 2, James White, Pete Mirrielees, Jonnie Hughes tries; Craig Sneddon 7 con), Zingari-Richmond 19 (Steve Roberts, Chris Bell, Jeremy Bekhuis tries; Ben Bradley 2 con).
Halftime: Harbour 43-19.
Referee: Liam Scanlon.
Kaikorai 32 Green Island 14
Captain Cameron Rutherford was a controlling influence and his accurate goal-kicking was invaluable as Kaikorai staved off a spirited challenge from Green Island at Bishopscourt.
Kaikorai eventually scored four tries to two and won by 18 points, but it was made to work hard by Green Island which competed tenaciously throughout.
Rutherford directed play accurately from first five-eighth and his five goals from six attempts allowed Kaikorai some leeway in what was a tighter contest than the score indicated.
Halfback Tomasi Palu was a dangerous runner and combined well with Rutherford while Richard Cowley was particularly influential when he moved into second five-eighth in the second spell.
Rob Griffiths was an all-action hooker and was rewarded with a try, lock Blair Tweed was good value in the tight and lineouts, and Adam Hill was a hard-driving No 8.
Ben Smith was inspirational for Green Island at second five-eighth.
He pulled off a try-saving corner flag try on Palu, made two clean breaks in midfield and was adept at feeding his outsides.
Sam Erepia and Albert Alapati were hard-running three-quarters, Alex Davies played tidily at first five-eighth ande flankers Jason Bint and Mika Mafi and lock Brett Campbell were the pick of the forwards.
Kaikorai 32 (Fetu'u Vainikolo, Tomasi Palu, Adam Hill, Rob Griffiths tries; Cam Rutherford 2 pen, 3 con), Green Island 14 (Sam Erepia, Jason Bint tries; Alex Davies 2 con).
Halftime: Kaikorai 18-14.
Referee: Ben O'Keefe.
