Captain Kian Belk scored his sixth goal of the tournament to give Wanganui the lead after 42 minutes, but Auckland equalised through James Stables eight minutes later, and then his captain Sam Lindberg scored at the death of the match to give his side the win.
It was more heartbreak for coach Andrew Spence, who for the last several years has taken teams who have done very well at tournament, but just come up short at the final hurdles.
"I think this year, we acknowledged we had a fairly inexperienced team," he said.
"We had nine new guys, so I'm satisfied with the effort.
"These boys that come through next year will be mentally harder."