Coach Declan Edge's young side emerged in the second half looking fresh and confident, stringing passes together and hunting in packs, which paid off as substitute Mohammed Awad, then Jason Hicks scored with 5min to go.
The loss leaves Otago in fifth place on nine points, still straining for a place in the ASB Premiership playoffs.
Otago had a good first half, and should have wrapped the match up, but a booming shot from Sam Mepham rebounded off the Waikato post, and several other good chances were not taken.
Possibly the absence of striker Ant Hancock due to a calf strain in the pre-match warm-up did not help Otago's finishing power.
Otago adopted a high line of defence that forced errors from Waikato, and gave coach Richard Murray's side lots of turnovers, but even the reliable Darren Overton missed a sitter, which might have been influential in his last match for United.
Otago worked very hard in the first half, but lacked the authority of a Mike Cunningham to steady the ship, and some wayward passing minimised the threat to Waikato keeper Mark Fulcher.
Waikato had not played at top level for a month due to matches in the North Island being rained off, but a recent game against a touring New Caledonian side produced six goals, and obviously gave the side an attacking edge.
Yet Otago was well served by youngster Joel Stevens, and throughout the match shots were launched by new fullback Harley Rodeka, Regan Coldicott, Donnie MacGregor, Overton and later James Govan.
The long-range shots were possibly indicative of Otago running out of ideas, and few quality crosses tested the Waikato defence which was well led by the experienced Michael Mayne and Josh Greene.
The critical period was at the start of the second half when Waikato's confidence grew, and Otago started to look leg-weary.
And it was tired defending that failed to clear a left-wing cross after keeper Peter Evans had blocked a shot from Adam Thomas, and in the resultant melee, Awad darted in to score from close range.
Otago still looked capable of getting at least a draw, and launched several attacks, but Jason Hicks pounced on a slack pass back and kept his cool to beat keeper Evans in the 85th min.
Coach Edge was happy with his team's performance.
"We deserved the win, against an Otago side that worked its socks off," he said.
All products of the Football Academy that Edge runs fulltime, the Waikato side's daily training showed out in the final quarter.
"We believe in the 10,000 hours target to achieve professional level skills. Those lads have clocked up 4000 hours, and are on track."
For a clearly disappointed Otago coach Murray the result was a case of not taking the early goal-scoring chances, and possibly there will be another team reshuffle before playing Wellington next Sunday at the Caledonian Ground.
A late headed goal from Tim Brown proved the winning difference for Wellington Phoenix against Gold Coast United at Skilled Park last night.
Brown struck his fourth goal of the A-League season in the 88th minute of a scrappy match.
The Phoenix remains in fourth and Gold Coast last on the competition table.
Otago v Waikato
The scores
Waikato - 2
Mohammed Awad, Jason Hicks
Otago United - 0
Halftime: 0-0.
