The Aucklanders were ruthless on attack and were good at the offload and securing turnovers, and after leading 24-8 at half-time, skipped away in the second half, with winger Victoria Grant picking up four tries in the match.
The loss ended Otago's season, with the team failing to make the semifinals for the first time and scoring just the one win, against Wellington in its first game.
Auckland, coached by former Wellington loose forward and Auckland Warrior Gavin Hill, qualified top of the table, winning all of its games.
It will play Hawkes Bay in one semifinal, while Manawatu will face Canterbury in the other.
Otago coach John Kyle said Otago showed plenty of courage but was outgunned by a better and more ruthless team.
He felt the side had let itself down by not making the semifinals.
Too many players probably thought it was going to happen by simply turning up this season.
Injuries did not help.
Kyle, in his third year of coaching, said he was unlikely to coach again next year.
The home side, though beaten heavily, showed plenty of courage and had its moments.
It was exceptionally good at taking the ball up on the drive and should have been rewarded for its efforts in the opening minutes of the second half.
Auckland conceded four free kicks in a row within 5min of the restart in trying to defend its line, and why referee Andrew Rowland, of Southland, did not go for a yellow card was a mystery.
But Otago got nothing for its efforts and eventually Auckland swung back on to attack and hooker Karena Penitio scored under the posts.
Captain and lock Vicky Heighway had plenty of pace around the field, while flanker Justine Lavea secured many turnovers.
Grant was quick and too slippery for the covering defence.
Otago captain and hooker Beth Mallard was aggressive on the drive and never took a backwards step, while loose forwards Rebecca Mitchell and Kerry Stoddart made metres when taking the ball up.
Halfback Zoey Berry threw some solid passes and wing Carla Hohepa was always a threat with the ball, using her speed.
She scored her first try with a fine 30m run, and then ran through to collect Berry's kick over the top to dot down midway through the second half.
Hohepa scored eight tries in Otago's five games.
Auckland 48 (Victoria Grant 4, Hannah Porter, Vicky Heighway, Karena Penitio, Faanati Aniseko tries; Porter 4 conversions), Otago 13 (Carla Hohepa 2 tries; Victoria Nafatali penalty goal).
Half-time: 24-8.
To complete a miserable 24 hours for Otago sides at Carisbrook, Tasman B beat Otago B 29-16 on Saturday, after the women's match.
Otago missed vital tackles, and threw away many opportunities.
It was Otago's first loss of the competition.
Tasman B 29, Otago B 16 (Cam Goodhue try; Glenn Dickson conversion, 3 penalty goals).
Half-time: 10-6 Tasman B.
