Ex-Auckland players Luis Corrales and Ian Hogg couldn't convert penalties for Team Wellington, ending its hopes of a maiden win after the scores were locked 1-1 after fulltime and extra time in Suva on Sunday.
Angel Berlanga also missed a penalty for Auckland but his team-mates were all on target and they celebrated wildly when Daewook Kim slotted the winner.
There were ugly scenes soon afterwards, when both teams came together in an ugly melee which took several minutes to separate.
The all-New Zealand final was a combative one, with Wellington midfielder Chris Bale sent off during extra time for protesting after a penalty was awarded to Auckland City. The penalty from Darren White was saved by Michael O'Keeffe.
Spaniard Tribulietx paid tribute to his team's discipline in a overly physical final.
"Unfortunately it was a little bit too much but both teams wanted to win the prize, there's a lot at stake," he said.
"I think we deserve it, it's been a very tough season for us."
Team Wellington counterpart Matt Calcott was disappointed with the attitude of some Auckland City players after the game, accusing them of poor sportsmanship.
"That sort of thing shouldn't carry on, to be honest, people chucking drink bottles," he said.
"But congratulations to them. They're set the benchmark over the last few years and they're got through by the skin of their teeth."
It is the seventh Oceania crown for the partly-amateur Auckland club, which wins another trip to the FIFA club World Cup, in Japan in December.
It shocked far bigger clubs at last year's event in Morocco, finishing third.
A 14th-minute penalty from forward Joao Moreira was reward for Auckland City's greater possession in the first half.
It conceded its first goal of the tournament when All Whites defender Hogg lashed home the equaliser six minutes from the end.
Auckland City's five consecutive wins - all under coach Tribulietx - equals the Champions League record of Spanish giant Real Madrid, which won the European title from 1956-1960.
Only Real Madrid (10) and Egypt's Al-Ahly (eight in Africa) have won more titles in total.
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