Otago's odds lengthened after 40 seconds, yes 40 seconds, when defender Tom Sadd was sent off by referee Mirko Benischke for fouling the flying Lucas Dakota just outside Otago's penalty area.
A crowd of Otago players disputed the decision and Benischke trotted over to the nearest assistant referee for a talk, then went all the way across to his other assistant, Fifa-qualified Brent Best.
A hushed crowd wondered if the referee had changed his mind, then burst into laughter as the embarrassed official borrowed some disciplinary cards from Best then trotted back to the scene of the misdemeanor and flourished a red card that barely matched the colour of his face.
However, it was no joking matter as Allan Pierce laced his free kick past keeper Adam Highfield's arms and Waitakere was 1-0 ahead.
Down to 10 men, Otago - which was already without Andy Coburn, Tim Horner, Alistair Rickerby and Ant Hancock - faced an uphill battle against coach Neil Emblen's top side, which has now clinched the championship.
It took another 20 minutes before Waitakere pressured a penalty that Pierce laced past Highfield's fingers.
Highfield was captain for the day, and went on to play a key part in denying Waitakere any other goals. The big keeper did it all, leaping high to cut out crosses and corners, and urging his side on to greater efforts.
Waitakere did hit the woodwork twice and was a smooth unit full of pace and guile, but Otago's defence, superbly led by Tristan Prattley and with Tom Connor in dynamic form, did not give a millimetre.
Ploughing a lonely furrow in attack, Chris Anderson held the ball up to give respite, and veteran Paul Seaman and James Reichwein slammed on tackles in midfield.
Morgan Day had flashes of real class, James Govan never stopped running, big Liam Lockhart grew another foot, Harley Rodeka clocked up miles and substitute Sam Mepham never gave in, but once again, failure to retain better ball possession cost immense energy.
Throwing caution to the winds in the last quarter, coach Malcolm Fleming brought on assistant coach Aaron Burgess and, with a tail wind, the striker added some menace to Otago's sporadic attacks.
Burgess hit the jackpot with a 94th-minute goal, snatched out of a hectic goalmouth scramble, and it was a tribute to Otago's fine, never-say-die effort.
Coach Fleming said, "Against the best team in the country, we could say we won the second half 1-nil with just 10 men. A superb effort. I am proud of them."
Coach Emblen smiled wryly and said, "We came to win and did that, but Otago frustrated us, and defended very well despite having 10 men.
"I prefer to concentrate on our performance. Ryan DeVries and Dakota Lewis were our standouts, and I am delighted that we have beaten the old competition record of 36 points."
