The home team led 10-3 at half-time, but openside flanker John Noonan scored a decisive try within the last five minutes to secure victory for the visiting side and collect the 20-year-old silverware.
''Very proud of the way we played. The young boys really stood up and it was a great team effort,'' Arrowtown coach Hayden Finch said after the game.
''We just made a few too many wee mistakes in the last 10 minutes and that's just down to they're young and a wee bit inexperienced,'' Finch said.
Both teams had quite a few injuries, but were happy with the teams they fielded. Injuries could not be used as an excuse, he said.
While it was hard to single any player out, Finch said No 8 Eddie Sefo was ''outstanding''. He was great with the ball in hand, had a big game on defence and made some blockbusting runs.
Wakatipu coach Damian Petre said the deciding try towards the end of the game was ''probably one of the only things we did particularly well all day'' in an otherwise disappointing performance.
''We were pretty fortunate to get away with a win,'' he said.
Petre said Wakatipu struggled to get into the game on Saturday and Arrowtown dominated most of the time.
Nevertheless, Premiers' Toi Roberts carried the ball well and Stuart Vincent, on the wing, ran and carried well, he said.
Arrowtown gets back to training today to prepare for Upper Clutha in Wanaka on Saturday at 2.30pm.
Wakatipu Premiers take on Wakatipu Wanderers at the Queenstown Recreation Ground on Saturday at 2.30pm. The premiers defend the White Horse Cup at home against Cromwell on May 18.
