All White David Mulligan scored twice for Auckland, but Otago coach Malcolm Fleming was heartened by aspects of his side's performance.
"For almost an hour, we kept them out, and during that time Otago had several chances to go ahead," Fleming said.
"Our team performance was superb, but the final result was a disappointment. We deserved better."
In an understrength Otago side there were many excellent performances, even without captain Tim Horner, the experienced Paul Seaman and striker Alistair Rickerby.
Goalkeeper Adam Highfield took over the captain's mantle, and rewarded Fleming with a string of top-class saves, the best a twisting volley at zero range from South American striker Luis Corrales that Highfield superbly reflexed away.
A magnificent work rate elevated Tom Sadd, James Reichwein, Tom Connor, Harley Rodeka and eternal motion machine Andy Coburn into inspired mode.
Chris Anderson and James Govan worked tirelessly against the odds in attack, creating half chances and also running defensive lines that pushed Auckland into uninspired passing sequences.
Auckland keeper Jake Spoonley also had to show his pedigree with high takes and brave battling among the boots as Otago pressured free kicks in the goals area.
Justin Prattley delivered several left-sided set plays that had Auckland scrambling, as international Ivan Vicelich marshalled his big experienced defence.
But there was no doubting Auckland's class on the ball, with former Otago player Stu Kelly masterminding midfield and scoring a goal of television quality as his shot arrowed into the top right corner of Otago's goal.
Mulligan used minimum time and space to open the scoring after 52 minutes in a crowded Otago penalty area when he drilled the ball through a tackle and in off the underside of the crossbar.
Mulligan made it 2-0 from the penalty spot seven minutes later, and it was a test of character for Otago as the home side chased shadows against Auckland's elaborate possession play.
Yet Otago's immense work rate, snapping at heels and stealing the ball, allowed another half a dozen decent chances for Govan, Anderson, Ant Hancock and later Aaron Burgess to get Otago on the scorecard.
Auckland coach Arron McFarland complimented Otago's spirit and admitted he had some foreboding that the home side would repeat its first-round 0-0 draw.
"Our goals eventually settled us," he said.
"And their quality was top drawer. I would have settled for more ordinary attempts, but the crowd appreciated those top-quality strikes."
Otago's Fleming was like a bulldog chewing a wasp: happy with his team's performance and several fine individual efforts, but disappointed not to get the elusive points required to move nearer a top-four placing.
