Waikato, who won in 2002 and 2005, finished on three-over par, in the annual event that pits teams of five from the 15 provincial districts in a 72-hole strokeplay competition with the best four scores counting each round.
Waikato made their move with an even-par 288 in the morning round in the rain to push their lead out to 15 shots over Northland.
North Harbour made the only serious run at the leaders in the afternoon, moving to within nine shots midway through their round, although their charge washed away in the wet on the back nine.
Harbour held on for runners-up on 18-over par, with two-time winners Wellington a further two shots back.
Auckland made a strong move with an outstanding two-under par 286 in the final round, played in heavy rain at times, to jump up to fourth place ahead of Northland, who will be delighted with their progression in the top division.
Canterbury finished sixth ahead of hosts Bay of Plenty, with Hawkes Bay, Southland and Taranaki rounding out the top 10.
Lee was the outstanding individual. The New Zealand amateur champion, who won the Bledisloe Cup for leading amateur at last month's New Zealand Open, started 2008 as he finished last year.
He made nine birdies yesterday, making a total of 19 birdies in all over his four rounds.
- NZPA