Auckland won 35-29 after leading 27-14 at the break, in a match with plenty of movement and enterprise.
The Otago side rallied well in the second half and, riding on the back of an outstanding individual effort from loose forward Naulia Dawai, was right in the match until the final whistle.
Dawai scored three tries, just one of four players to score three tries against Auckland at Eden Park, and was into everything in what was his first start of the season.
The big Fijian was immense on attack and popped up all round the field as Otago hung in the match and actually came home stronger.
Otago coach Cory Brown had mixed feelings after the final whistle.
''No one likes losing and the boys are a bit down. But they played fantastically well,'' he said.
''They were up against big powerful men and a lot of established Super rugby players.
''But we have got some reasonable rugby players who can play up to that level. We've just got to keep learning from it, both as individuals and as a team.''
He said Otago knew Auckland would look to move the ball and so there were opportunities to grab turnovers, which the side did.
The Otago set piece was solid and, if the kickers had knocked over the conversions of its four tries, then Otago may have scored an upset victory.
But the radar was not on and Auckland came away from the game with five points.
Otago hung tough against the big solid Auckland pack, was aggressive in the tackle and grabbed some turnovers at crucial stages.
Right on fulltime, winger Jack Wilson found some room on the outside, Otago replacement halfback Kaide Whiting received the ball about 40m out and a miracle try looked to be unfolding.
But Whiting was run down, the ball was spilt and Auckland managed to clear.
It was Auckland's third game in nine days and there were clear signs the side was running out of juice as the match went on.
Brown praised Dawai but also the work of the forward pack, which helped create the tries for the Harbour man.
Auckland had started with a hiss and a roar and had three tries within the opening half hour.
But Dawai barrelled over from 5m out just before halftime for the first of his tries.
He scored two more within the opening 10 minutes of the second half as Otago roared back into the game.
Dawai then created a try for Wilson, with a nice offload drawing in two men.
Apart from Dawai, prop Hisa Sasagi played well, while Michael Collins tackled well in the backs.
Hooker Sam Anderson-Heather was forced off for Otago with a badly injured ankle at halftime and is doubtful for Thursday night's game against Wellington in the capital.
Otago v Auckland
The scores
Auckland 35
Charles Piutau, Mitch Karpik, Akira Ioane, George Moala tries; Simon Hickey 3 con, 3 pen
Otago 29
Naulia Dawai 3, Jack Wilson tries; Fletcher Smith 3 pen
Halftime: 27-14
