There may have been locals expecting a goal rush from coach Neil Emblen's side which has yet to lose this season and looks unstoppable with eight straight wins from eight matches.
The outlook looked grim for the visiting side when after just two minutes, Allan Pearce hooked over a corner and under pressure, Otago's reliable Adam Highfield watched the ball end up in his net.
So coach Malcolm Fleming's side had to dig deep as partisan Waitakere supporters bayed for blood, and the slick Auckland side swept forward.
Without the suspended Andy Coburn and centreback Tim Horner, Otago's ranks looked thin, but the muscular Paul Seaman dropped deep while Liam Lockhart and Tom Sadd battled away centrally, and fullbacks Tristan Prattley and Tom Connor conceded nothing as Otago stemmed the tide.
Before kick-off Nathan Knox, in his last match for Otago before leaving for Australia, was presented with his ASB Player of the Month award, but it was striker Phil Ruggles who caught the eye with a series of early attacking runs.
In the sixth minute Ruggles was flagged on a hairline offside call, then two minutes later it took a full-stretch tackle by Tim Myers to thwart the Englishman.
But in the 12th minute, Ruggles' industry was rewarded when he broke through the Waitakere ranks and kept his head to equalise at 1-1.
Waitakere's pace via Roy Krishna, Michael Gwyther and Chris Bale exposed gaps in the Otago defence, and keeper Highfield redeemed himself with a series of fine saves.
Fullback Connor showed his class with a perfectly timed goal saving challenge on Pearce, but was hurt in the process, and had to be subbed in the second half.
However to be level at halftime, after fighting back from that early goal gave coach Fleming a boost for his halftime team talk.
Waitakere continued after the break with more ball possession, but on the bounce, Ruggles created another couple of goalscoring chances. First he found space to chip to Seaman who shot at goal and then he hammered a shot on the run that trimmed the Waitakere crossbar.
But it was the home side that broke the deadlock after 58 minutes, when Pearce crossed from the left and Gwyther made the score 2-1.
Coach Fleming introduced fresh legs replacing Alistair Rickerby with Aaron Burgess and Morgan Day for Ruggles.
Otago played some flowing football at that stage, but failed to get shots on target. Then it was player-coach Emblen who pounced on a defensive error to score in the 90th minute and create a slightly flattering 3-1 score to Waitakere.
After the match, Otago counted the injury toll with Ruggles nursing a sore jaw, similarly Rickerby left the field with a suspected broken collarbone, and Seaman's exhausted exit reduced Otago to 10 men in the final few minutes.
Coach Fleming said the last thing the team wanted was to concede an early goal, but it showed great resilience in hot conditions to climb back and equalise.
"Nathan Knox as always was a real force for us and Phil Ruggles did well until he was injured. He may have a broken jaw, after a collision," Fleming said.
"Waitakere are a class side, but we kept them more than honest in the second half, and with a little bit of luck might have grabbed a share of the points."
