Referee Darren Sundborn was unsighted as a barrage of close-range shots peppered the crowded Waikato goalmouth, the last bouncing off keeper John Fletcher's crossbar and angling down towards the goal line.
Sundborn consulted assistant Kenny Evans, who said the ball had not totally crossed the line.
The ASB Premiership match was delayed due to a late inward flight, but Waikato was switched on enough to score a superb goal after six minutes, when former youth international Jason Hicks laced a 25m shot into the top left corner of Otago's goal.
On his debut for United, keeper Adam Highfield produced a full-length dive and got his fingertips to the ball but could not prevent the goal.
Highfield had a fine match which included a couple of elastic saves that kept Otago hopes alive.
He was rarely troubled, for while Waikato's quicksilver attack strung together passes and showed real pace, it ran into some battering tackles.
Regular Otago midfielder Andy Coburn did not play due to a calf injury that surfaced at training, but steady matches by team captain Tim Horner and fellow centreback Tom Sadd cut off options, and fullbacks Tristan Prattley and Hayden Gunn defended well, then pushed forward.
New midfielder Paul Seaman slammed on a couple of fierce tackles that earned a yellow card, and fellow linkman Matt Thomas covered ground and did well.
Flashes of brilliance from young Ant Hancock and Harley Rodeka produced shots and robbed Waikato of confidence, but, as coach Malcolm Fleming will once again stress at training, too many passes went astray.
In the second half, Waikato's German coach, Willy Gerdsen, lost his cool and became very animated as he shouted advice to regain team shape.
A one-goal margin always produces tension, and Otago fed on that with sustained pressure and many set plays, while Waikato's pacey attack of Hicks and Nathan Palmer threatened to slice through on counterattack.
Targetman Phil Ruggles rarely got the service he needed, but in swarming attacks Otago burst through the Waikato ranks and threatened an equaliser.
Nathan Knox slipped several tackles to shoot, Rodeka and Hancock found space, but Otago's best chances came through corners and free kicks before the refereeing decision reminiscent of the 1966 World Cup incident in England.
Fleming was understandably sombre after the match.
"As long as we give away possession with bad passing, and try to run with ball too far, we will struggle this season.
"We were doing things we do not do at training, and that's disappointing. Waikato are not a great team, but they were better than us and deserved to win."
ASB Premiership
The scores
Waikato 1(Jason Hicks)
Otago United 0
Halftime: Waikato 1-0
