Striker Dave Dugdale pounced after just three minutes to turn in a left-wing cross and, at 1-0, Otago played confident football and should have gone further ahead.
But the mature Waitakere side regained composure and started to play to its strengths, with the fleet-footed Roy Krishna and Benjamin Totori looking sharp in attack.
Otago started with Mike Abbott recruited to offset the loss of regular captain Tim Horner.
Things worsened when Tom Sadd limped off injured and Otago's team shape wobbled.
Referee Mirko Benischke struggled to take into account the wet, slippery conditions and fragmented the match with six yellow cards for tackles more enthusiastic than dangerous.
Just after Dugdale headed a good chance over Waitakere's crossbar, the visitors equalised in the 13th minute.
After a trademark darting run up the middle by Totori, the Solomon Islands international, gave keeper James Waggett no chance with a strong shot.
Waitakere player-coach Neil Emblen later replaced Totori with Aaron Scott to steady his team shape.
"Both sides were attacking all over the park, and I felt we needed more stability so we returned to a 4-4-2 formation," Emblen said.
In the second half, Waitakere started to win greater ball possession, especially as tackles by Stu Kelly, Andy Coburn and Abbott were punished by the referee.
Yet there were many sharp attacking moves by both sides that should have produced goals.
Krishna dazzled with some elaborate runs but he was channelled wide by the Otago defence, which was well organised by Chris Jenkinson.
Kelly set up several clever passing moves that included Ryan Faichnie, Dan Ede and the mobile Dugdale, but Emblen towered in defence and cut out most high balls.
Otago's tallest player, Nathan Knox, made some incisive runs, arriving late at pace, but Waitakere's defence and keeper Danny Robinson closed ranks.
A series of free kicks - one given by the referee because Waggett held the ball for longer than six seconds - had Otago defending for extended periods.
The game became a question of Waitakere pressure versus Otago breakaway attacks and, as legs got heavy, a misplaced pass out of defence allowed Krishna to drive over a low cross which Brent Fisher rammed home in the 78th minute.
Disconsolate Otago coach Malcolm Fleming refused to comment on what some felt was an erratic referee's performance, and questioned his side's fitness in the last quarter when it mattered most.
"If you do not put your chances away and score goals, it makes things difficult. We had our chances and didn't take them," Fleming said.
