The sustained period of pressure payed off for Waikato right as the first half buzzer sounded, with winger Tyler Campbell crossing over in the corner through a perfectly constructed set piece for their second try.
It was more of the same for Waikato in the second half, with prop Toby Smith eventually making it a one-point game – after Fletcher Smith's conversion – with a 50th minute try.
But Otago would later earn a couple of penalties in quick succession at the other end, ultimately proving to be the difference in the game.
After opting against going for goal moments earlier, on a second Waikato penalty in the kicking zone, Otago's No 10 Josh Ioane – who strikes the ball as purely as anyone in the country – decided to take the points and slotted over a crucial three-pointer to put Otago ahead 23-19.
And that score would remain, after a mammoth second half defensive effort from the Blue and Gold, fending off a dogged Waikato to hang on for a famous victory.
"It is I guess the old cliché, we had to come in and attack and we did," said Otago skipper Michael Collins after the game. "And then we closed it off at the end to sneak away with a win so yeah I'm so proud."
Earlier, Bay of Plenty ended their Mitre 10 Cup season on a high with a 38-35 win over Northland in Tauranga.
But it will be Northland who will play in the Championship semifinals after finishing fourth, and will play Waikato – who finished top of the ladder despite the loss – in Hamilton next week.
In the later game, Canterbury claimed a 19-14 victory over Counties Manukau in Pukekohe.
The win was bitter-sweet for the Cantabrians as they failed to get the bonus point victory they needed to move ahead of Auckland – who play tomorrow against North Harbour – in the Premiership ladder.
Otago 23 (Mitchell Scott, Josh Dickson, Joketani Koroi tries; Josh Ioane con, 2 pen)
Waikato 19 (Josh Iosefa-Scott, Tyler Campbell, Bailyn Sullivan tries; Fletcher Smith 2 con)
HT: 20-12
