The home side had seemingly wrestled control of the match, clearing out to a 45-39 lead with 15 minutes remaining.
But Waikato, led by midcourt duo Jessica Tuki and Elias Shadrock, and impressive shooter Elsa Brown, clawed its way back into the game and recaptured the lead with just over a minute remaining.
Otago potted a shot in the dying moments to avoid defeat and, in the end, was lucky to escape with a draw.
Coach Deb Tasi-Cordtz said the draw felt more like a loss.
"It does. Especially because we had the lead and I thought we were the better team," she said.
"But there was just this patch of about four minutes that they got the better of us.
"I think we shut down. We got a bit anxious when they got a bit of a roll on and we didn't let the ball go as we had been, and we were a bit tentative in our movement. It just showed under pressure we cracked."
Otago's build-up was disjointed to say the least. Storm Purvis, Zoe Walker and Te Paea Selby-Rickit were away with the New Zealand under-21 team and did not return until Thursday.
Fellow New Zealand under-21 representative Stacey Peeters returned home early but only because she picked up an injury, and former Australian international Demelza McCloud was overseas on a planned holiday and also returned on Thursday.
Not surprisingly, Otago started like a team of players who had just met each other. The connections were sadly lacking, with passes going to space rather than a team-mate. Waikato stole a march, racing to a 5-1 lead.
"We knew our build-up would be like that and [we] had been doing a lot of individual stuff and did not want to use it as an excuse," Tasi-Cordtz said.
"We did lack those connections, I guess, but they did come."
Midway through the opening quarter, Otago's class started to shine through and the province scored the last four goals to a take a 15-14 lead into the break.
Waikato responded with three unanswered goals at the end of the second period to level the score 27-27.
Kate Shearer replaced Olivia Bates at goal shoot and made an immediate impact with her pace and willingness to put up shots.
Otago seized the momentum with a five-goal run. The gap grew as large as nine goals but the visitors finished the period stronger, closing to six.
Waikato pegged back another few goals and, with five minutes left, was within striking distance and had all the momentum.
Selby-Rickit was deservedly named player of the day. She moved beautifully in the shooting circle and showed the benefit of an extra year with the Steel.
Purvis was outstanding in the first half, picking off intercepts with ease.
Shannon Francois got through a lot of work and was steady, and Shearer played with good energy.
McCloud had her moments but looked rusty. Midcourter Gina Crampton had an off game and Bates made some nice passes but lacked pace and only put up two attempts in 30min.
Netball champs
The scores
Otago 56
Te Paea Selby-Rickit 45 from 48, Kate Shearer 11/15, Olivia Bates 0/2
Waikato 56
Elsa Brown 31/37, Jessie Waitapu 20/25, Hayley Stockman 5/8
Quarter 15-14, halftime 27-27, third quarter 45-39.
