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The team of four finished with a total of 222, nine shots ahead of Otago Boys' High School.
Otago women's representatives Sumin Kang and Danielle Bailey shot 74 and 77 respectively but their scores were adjusted down by two shots due to the difference in the course rating for men and women.
Wakatipu No.2 Liam Judkins chipped in with a gross 75 to ensure the team's success.
The allowance for the two girls was not required as Wakatipu would have won by five shots without the reductions.
Year 10 pupil Seb Kyle was the best of the Otago Boys' golfers with 75 while Joseph Hancock came back strongly with a par 36 back nine for 76.
John McGlashan College finished a further 15 strokes back in third place, Callum White featuring with a two over par 74.
As the best girl, Kang will attend the national Eagles final in Te Awanmutu in September and White will also attend that final.
There was a sudden death playoff to find the second boy to attend the final - Liam Judkins (Wakatipu) parring the playoff hole while Otago Boys' Seb Kyle three-putted.