Clarke won two from two on the final day, beating two previously undefeated golfers in the process.
Auckland had won all their games throughout the week until they met Northland in the final - their first appearance in the final stages since the tournament's inception.
"We just worked as a team all week and it really came through in the end. We actually worked as a team instead of a bunch of individuals. We just stuck together."
He said despite poor conditions earlier in the week, the team were able to hang on for some key wins until the weather perked up on Thursday, allowing Northland to hit their stride.
"We've had so many good players before us try and get there but we're the first ones to make the final and first ones to win so it's pretty special."
Team manager Vaughan Witten said he knew Northland had made history as he was on the final hole.
"I was walking down the last hole with Taylor Gill and I knew we had won and I said, 'Mate, we've just won the Toro!'."
On the final day of round-robin play, Northland held their nerve to win the necessary tie against Canterbury while Southland's win over Otago enabled Northland to go straight through into the final stages.
"We knew if we knuckled down and keep it close, we'd have a shot and when the pressure came on, we delivered," Witten said.
"Many people have tried their best to bring home that trophy and we're just stoked for those people who this win is for."
After squeezing into the final four yesterday, Northland used that momentum to carry them home and write one of the great underdog stories at the Clearwater Golf Club.
Northland were strong during their six round-robin games throughout the week. They started on Monday with a strong 5-0 drubbing of Hawke's Bay before losing narrowly to Otago 3-2, with Clarke and Neely picking up wins.
After a bye on Tuesday morning, the team beat Tasman 4-1 in the afternoon with Clarke winning strongly with five holes remaining. The sole round on Wednesday saw Northland beat Southland 4-1.
Thursday featured what would become a practise run for the final with Northland losing to Auckland 4-1, Neely claiming the solitary win.
The last of the round-robin games saw Northland earn a must-win victory against Taranaki 3-2, Brown winning with four holes remaining.
This sent Northland into the semifinals along with powerhouses Canterbury, Wellington and Auckland.
Northland drew the hosts in what was to be a tight match-up. Northland narrowly edged out the 3.5-1.5 victory with Clarke leading the way, winning with four holes remaining and Gill and Brown finishing one-up at the end of their rounds.
The final between Auckland started well for the Northlanders will all golfers either taking a lead or staying level. Mid-way through the round, Auckland surged back to bring it to a level playing field before Northland pulled away to claim victory.
The Toro Women's Interprovincial tournament is next week in Christchurch.
