Bay started the final round one shot behind Southland but finished earlier yesterday afternoon while the local team had to graft hard in the strengthening winds.
The win came despite New Zealand representative and Southland No 1 Vaughan McCall carding a 3-under 69 for the lowest score of the final round.
Waikato finished in a tie with Manawatu-Wanganui for third while Otago was next in fifth.
With rounds of 69, 74 and 71, Waikato No 1 Luke Toomey took the individual title, finishing 2-under-par on 214.
The top amateurs and five trainee professionals faced horrendous conditions on Saturday as strong winds, torrential rain and hailstorms provided a real test.
Add to this the tiger rough which had not been cut for four weeks and low scoring went out the window.
In the conditions, New Zealand's top-ranked amateur and Auckland No 1 Tae Koh carded a 15-over 87 in the opening round while defending champion Auckland finished second bottom on 313.
Waikato took the early lead as Toomey finished 3-under on 69 and No 2 Nick Coxon on par figures.
Southland was one shot back with No 3 Tyler McLean and No 4 Scott Hellier finishing 1-under on 71.
Hellier turned 4-over and carded five birdies coming home for 31 for a stunning turnaround to help the local team's cause.
First-round play ceased at 1.30pm on Saturday while Otago was still on the course along with the abandonment of the second round.
The Otago golfers spent 90 minutes in the clubhouse while the greens were swept and then went back out at 3pm to complete their rounds.
After the second round yesterday morning, Southland held a one-shot lead over Bay of Plenty and Waikato, with Manawatu-Wanganui fourth and Canterbury fifth.
Otago had slumped to sixth having to count a 7-over 79 in the second-round team total.
But the final round came down to a two-way battle of attrition between Southland and Bay of Plenty as Waikato drifted out of contention.
Otago showed some fighting qualities in the final round after a slow start.
Brent McEwan fought back from 4-over to 2-over while No 2 James Anstiss also made two birdies to go from 3-over to 1-over.
No 3 Duncan Croudis came back from 4-over to 1-over while Nick Borren was square for most of the round and Mark Brooks grafted well to finish at 2-over.
The Otago golfers found it difficult to hang on to their improved mid-round scores as the exposed 15th, 16th and 17th holes were lashed by strong winds.
However, Otago's fifth place is better than it has been in recent years although this team's forte is no doubt in the matchplay format of the game.
This augurs well for Otago's chances in the interprovincial team tournament in Hamilton during the first week of December.
The five-man team in playing order and the reserve will be named by selection convener Greg Johnson in Dunedin this morning.
