The Kangaroos remarkably never led until Cam Zurhaar kicked a goal after the final siren on Saturday at Marvel Stadium, sealing the 17.9 (111) to 16.9 (105) win.
After several near-misses this season and last week's debacle against Adelaide, this is a massive scalp for the emerging Kangaroos.
"I'm so rapt for the club and certainly the playing group," said Clarkson, North's coach since 2022.
"I'm just so pleased that we were able to find a way and continue to have belief.
"We've been competing a hell of a lot better (this season) ... not quite getting there against high-quality opponents.
"For us to get that scalp was a bit of justification for a lot of hard work that's been done. But we know we're not there yet."
By contrast, Suns coach Damien Hardwick was bitterly disappointed that his side stopped attacking with about 10 minutes left, ultimately sealing their fate.
Gold Coast kicked the first three goals of the game and led by 43 points late in the second term.
"If you stop playing offensively - there's only one side trying to attack - you're on the back foot," Hardwick said
"That's a number of things. It can be fatigue, it can be mental fatigue, it can be physical fatigue.
"The worst thing about it is we have to sit on that loss for nigh-on two weeks."
North and Gold Coast have byes next weekend ahead of massive clashes - the Kangaroos next play Fremantle in Bunbury, and the Suns face reigning premiers Brisbane.
The Suns were coming off two wins in Darwin, but have a history of struggling immediately after their Top End games.
Clarkson made sure that was in the heads of his players after they had kicked four goals to one in the third term to put themselves back in the game.
"We mentioned it at three-quarter time ... maybe these guys might be tired from Darwin, who knows," he said.
"We just knew if we continued to play our method, we'd give ourself a chance."
Clarkson said much of North's method was stacking up in the first half, but they had conceded five goals from centre-square ball-ups and he noted that was "world-record pace".
So a few adjustments were made at the long break, plus two crucial moves - Zurhaar out of defence and back into attack, while Colby McKercher was moved to half-back.
Zurhaar in particular was crucial, and he was mobbed by teammates after kicking the winning goal.
In a game marred by too many contentious umpiring decisions, Oscar Adams gave away an obvious free with seconds left to set up Zurhaar for his triumph.
"They got the decision right, the most important one ... we take that and move on," Clarkson said with a chuckle.
Luke Davies-Uniacke, North's best player, goaled from a set shot with a minute left to tie the scores.
The Suns won the crucial centre clearance, but the Kangaroos rebounded off half-back. A long ball found Zurhaar deep in attack and Adams was penalised.
Jack Darling kicked three goals for North, while Jed Walter did the same for Gold Coast.
North's Jy Simpkin and star Suns midfielders Noah Anderson, Christian Petracca and Matt Rowell all stood out.
Suns key defender Sam Collins was again superb.
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