The defending champion lost 43-10, after being down 14-5 at half-time.
Maniototo by and large starved Wakatipu of the ball and, guided by veteran first-five and goal-kicker Charlie Hore, outplayed the home team in both the forwards and the backs before a large crowd at the Queenstown Events Centre.
Wakatipu scored the opening and closing tries, to Adam Baird and Pita Wilson, respectively, but Maniototo piled on five tries, including four in the second half, in between.
Maniototo scored 29 unanswered points in the second half before replacement Wilson's try gave Wakatipu's score some respectability.
Until Saturday, Wakatipu had been unbeaten at home all season, though some of its wins were by the narrowest of margins.
It had topped the competition table and only suffered two losses - 27-7 to Maniototo in Ranfurly on July 6 and a one-point away loss to Arrowtown, two weeks ago.
Wakatipu, which won last year's final by beating Arrowtown, can console itself that it held on to the White Horse Cup this season and made the final for the second year running.
Captain Regan Pearce - who flew back to Queenstown from India on Saturday morning - said while it was not the way his side wanted to end the season, he had ''nothing but full respect for Maniototo''.
''They were an unbelievable team ... they certainly deserved that victory.
''We did say if we stayed in touch in the first half all we had to do was play a bit more expansively [in the second 40 minutes].
''But they just came back as strong - they knew our game plan and worked around us.''
Pearce, who has been plagued by injuries this season, spent Saturday night at Lakes District Hospital with a cracked sternum, sustained late in the second half.
However, he had not ruled out putting his boots on in 2014.
''I missed two games while I was in India, so I've got nine to play [to reach 100 for the club].
''I would love to achieve that, absolutely.''
Meanwhile, Arrowtown suffered its second loss in two weeks, being beaten by Cromwell 20-17 in the play-off for third and fourth in the top five.
Coach Hayden Finch said it was a disappointing end to the Bulls' season, particularly given they had a lead of 17-5.
''We ran into difficulties in the last 15 minutes.
''It would have been nice to finish with a win - it was kind of hard to get motivated, but we never want to lose.''
The Wakatipu Wanderers won its second division third-fourth play-off game, beating Matakanui Combined 23-12, at the Events Centre on Saturday.
