The home side started in great style, sweeping forward confidently to earn a 2-0 lead, but after Waikato hit back twice to equalise, it took a fine penalty save by Otago keeper James Waggett to preserve a point.
"We were lucky, and would have lost but for Waggs' excellent save," Otago coach Malcolm Fleming said.
"We initially played our best football for some time, to go two goals ahead, then slipped back into bad habits and had a terrible second half."
A surprise selection for Waikato was veteran defender Che Bunce in attack, and for a 34-year-old he did a fine job as targetman, initiating many controlled moves.
Former All White and Coventry City player Bunce was disappointed not to grab maximum points after his team fought back from 2-0 down.
"We conceded two early goals.
I think our heads were still on the plane at that stage, but it was pleasing to climb back into the match with some good passing moves," Bunce said.
In perfect conditions, Otago fans had plenty to cheer about as the blue and golds initially played some superb football, and after just seven minutes Ben Light drilled a low shot past keeper Alex Carr to open the scoring.
Otago used the ball well, varying short and long passing, and supporting the ball-carrier in numbers.
Nathan Knox had a busy game in midfield and was on the spot to finish another flowing move to shoot Otago 2-0 ahead after 17 minutes.
But the warning lights started to shine as Otago either ran the ball too much or sent passes astray, and Waikato's Michael Gwyther fed off Bunce and threatened.
In the 31st minute, Gwyther finished off a spell of Waikato pressure by scoring, then seven minutes later he powered into a melee from a right-wing corner and headed the equaliser.
Half-time team talks must have centred on whether the visiting team would remain in ascendancy, or whether Otago could play its way back into the match.
Waikato took the initiative, with steady pressure and a series of corners, and seven minutes into the half, left fullback Mike Abbott made a rash tackle on Bunce, wide on the byline, and referee Dave Langley pointed to the spot.
Former Otago player Joe Simpkins struck the ball well, but Waggett anticipated astutely and stretched low to his left to make a fine save.
Otago brought on fresh legs in Robbie Deeley, Tom Connor and Mike Smith, and while defender Smith pushed forward and hoisted a couple of dangerous balls into Waikato's goalmouth, there was more passion than playmaking in the closing stages.
Another missed penalty, this time by Manawatu striker Seule Soromon, heralded another 2-2 draw in Hawkes Bay, and Canterbury grabbed an important point in drawing 1-1 with top team Auckland.
Otago remains in third spot on 17 points, but Canterbury has two games in hand and sits in a handy position two points behind Otago.
The curtain-raiser at Carisbrook featured a 3-1 win by Otago United's under-20 team over Manawatu in the national youth league.
Manawatu took a seventh-minute lead by Dwayne Blackett, then Otago hit back with goals by Jackson Rodeka and Sam Mepham before Manawatu scored an own goal.
