Bay of Plenty's victory means Auckland, the inaugural champions, has not won the junior title since 2007.
The lads from the City of Sails will be disappointed with their fifth round performance when they were hammered 7-1 by Otago to hand Bay of Plenty the advantage.
Last year's runner-up North Harbour finished third, a further two shots back from Auckland on eight points.
The host province Waikato, who has finished runner-up in the past 14 years, completed a disappointing week when they finished in seventh place.
Most of New Zealand's best players - including Danny Lee, Josh Geary, Fraser Wilkin, Nick Gillespie, Mark Purser, Peter Lee, Tae Koh, Josh Munn and Tyler Hodge - have begun their golf careers in the Junior Interprovincial.
The eight-man teams were made up of five golfers under the age of 19 and three under the age of 16.
Junior Interprovincial
Cambridge Golf Club (win = 2 points, half = 1 point and loss = 0 points)
• 12 points Bay of Plenty, 10 Auckland, 8 North Harbour, 7 Northland, 6 Otago, Canterbury, 5 Waikato, 4 Manawatu / Wanganui, 2 Hawkes Bay, 0 Eastland