Just a week after copping a 124-point loss at the hands of Fremantle, Jack Darling's four first-half goals put the Kangaroos on track for victory in Saturday's match in front of 42,409 fans at Optus Stadium.
North led by 21 points early in the final quarter, but two goals to an inspired Jobe Shanahan and one to Waterman closed the margin to two points.
Then with a little over a minute to go, Waterman took a mark just 30m out and directly in front.
Waterman's set shot struggles have been a huge talking point this season and the 2024 All-Australian sent his 35m attempt into the post.
North took two strong marks after that to seal the 10.14 (74) to 10.13 (73) victory, with Waterman cutting a devastated figure at the final siren before giving away his boots to a kid in the stands.
"I understand that he (Waterman) gets the last go, but I think there's probably six or eight shots missed throughout that game that were pretty easy shots on goals for both teams," Eagles coach Andrew McQualter said.
"So me personally as a coach, I absolutely love that I've got a key forward having the most shots in the competition. What an absolute treat that is to be able to coach someone like that.
"I love how Jake's competing. He'll be riding the emotion of this, he's such a proud competitor and we're just going to support him.
"We'll just keep showing evidence of him competing and giving himself chances and we'll keep working with him on his goal kicking."
The result improved North's record to 6-7, but coach Alastair Clarkson conceded his team were fortunate to win.
"It's a fine line between pleasure and pain isn't it?" Clarkson said.
"I can't tell you I was overly confident that Jake was going to miss that shot. We were lucky to win in the end."
Darling finished with 4.1 in his biggest haul since kicking six goals against Gold Coast in 2022, while Nick Larkey kicked four in a welcome return to form.
Shanahan only had two disposals at halftime, but the Eagles spearhead sprang to life after that and finished with five contested marks and three goals.
One of those majors was a checkside from the pocket with just over two minutes remaining.
Waterman finished with 3.3 in a strong display that was only let down by his accuracy.
Kangaroos forward Paul Curtis could be in strife for his tackle that resulted in a heavy concussion to Hamish Davis just 10 minutes into the match.
Curtis had both of Davis's arms pinned when he tackled the Eagles utility to the ground.
Davis was wobbly on his feet when he was finally able to stand up, with the 20-year-old helped off the ground and playing no further part in the match.
