The major talking point of the first half came in the 13th minute, when Auckland were awarded a penalty. Wellington goalkeeper Michael O'Keefe had failed to clear a freekick and as the ball dropped loose, defender Bill Robertson was judged to have pulled down Auckland's Marko Dordevich inside the box.
It looked a harsh call and caught the ire of the Wellington squad who remonstrated passionately as Tahitian referee Norbert Hauata pointed to the spot.
But Auckland striker Joao Moreira kept his head and slotted the kick straight down the middle as O'Keefe flung himself to the left.
In the second half as Auckland tired, Wellington grew stronger. The O-League debutants seemed to catch a second wind buoyed by their pace advantage up front and took the game to Auckland with a never-say die attitude.
And just when it seemed like Auckland may have done enough to win, Wellington defender Ian Hogg popped up with a moment of brilliance, thrashing home a spectacular left footed volley from the edge of the box in the 79th minute to equalise.
Auckland goalkeeper Tamati Williams pulled of a stunning save in the last minute of regulation time to deny Michael Gwyther a left footed winner from the edge of the box.
In the second half of extra time Auckland were awarded another dubious penalty for handball inside the area.
Auckland striker Ryan De Vries fired a shot at Ian Hogg from point blank range and as the ball slammed into his elbow, Hauata pointed to the spot again.
Wellington defender Chris Bale was then sent off for his remonstrations, but watched on from the sideline in delight as O'Keefe brilliantly saved from Darren White's penalty.
Luis Corrales and Ian Hog missed spot kicks for Wellington, while Alex Feneridis, Cole Peverley and Justin Gulley scored and Auckland defender Angel Berlanga missed, but Marko Dordevich, Adam McGeorge, David Browne and Daewook Kim all found the net.
Korean import Kim's shootout winner sparked wild celebrations from the Auckland camp, who will earn a minimum of $659,000 for their appearance at the Club World Cup.
Auckland City FC 1 (Joao Moreira)
Team Wellington (Ian Hogg) 1
HT 1-0