The champions scored five tries in the final 40 minutes after some sterling defence by the visitors had held them to just a 10-8 lead at the break.
But that effort finally took its toll on Otago and in the final quarter Auckland ran riot with Brad Mika, Ben Atiga, Mils Muliaina and Taniela Moa adding to earlier tries from Keven Mealamu and Doug Howlett.
Auckland dominated territory and possession from the start but struggled to turn that dominance into points as Otago proved time and again why they held the best defensive record in the competition.
It was Otago who drew first blood with Josh Blackie beating a Joe Rokocoko tackle to dive over in the corner after a cut out pass from Nick Evans.
Evans could not add the conversion and Otago's 5-0 lead was threatened shortly afterwards as Auckland camped in their opponents 22, only for a knock on to deny Saimone Taumoepeau before Daniel Braid was held up over the line.
Brent Ward was eventually given the opportunity to reduce the arrears when he was on the receiving end of a dangerous tackle by Otago centre Neil Brew and the Auckland fullback fired the ball between the posts.
Evans pushed the score out to 8-5 in Otago's favour with his first penalty in the 24th minute and it was only some staunch defending that kept the men from the south in the game.
Ward, who had a poor night with the boot, missed a straightforward penalty three minutes later when Jerome Kaino was blocked chasing a through kick from Tasesa Lavea close to the Otago line.
Auckland, however, were rewarded for their persistence in the 32nd minute when a set-piece move from a five metre lineout saw hooker Mealamu power his way over the line and Ward's conversion from the sideline handed them the lead for the first time as they went into the break 10-8 ahead.
After struggling to breach the Otago defence in the first half, it took Auckland just seven minutes from the re-start to cross the try-line for the second time.
Again Auckland demonstrated great patience before a cut-out pass from scrum-half Steve Devine was juggled by Howlett, who dived over in the right-hand corner.
Howlett appeared set for a repeat performance in the 58th minute after an excellent burst upfield by Muliaina, only for Evans and Blackie to bundle the wing into touch a metre short of the line.
Evans then reduced the deficit to four points with a long range penalty on the hour but it was the final score of the night for Otago as the earlier defensive effort finally took its toll.
Two tries in three minutes to substitutes Mika and Atiga sealed the victory with 10 minutes remaining and a fourth try to Muliaina in his final game for Auckland and a solo effort from Moa was the icing on the cake.
Auckland skipper Justin Collins was delighted with the victory and insisted he had always been confident his side could pull off the win, despite the tight scoreline at half-time and a staunch defensive effort from Otago.
"I felt like things were reasonably under control for most of the first half. We had to keep battling away really. They [Otago] were superb in the first half, especially in the forwards.
"But we were running them around and by the time the second half came around I think they were blowing a bit and we really pushed them and things opened up after that."
Otago coach Wayne Graham conceded a lack of possession and fatigue had ultimately been his side's undoing.
"We came here with nothing to lose and we were going to give it our best shot no matter what.
"We couldn't get our game going. We couldn't get enough possession. I think we were living off 30% possession for most of the game and with 15 minutes to go the score was 15-11 and something was going to give.
"We had an opportunity to do it but with the pressure they had built up when the gates opened it was goodnight nurse.
"I think we ran out of steam. We defended for 75% of the game and we just started to fall off a couple of tackles and a few gaps started to open up."