The Bombers led by 26 in the second term but lost luckless defender Jordan Ridley to a hamstring injury just before half-time, and Harrison Jones to a horror lower leg injury in the third quarter.
Jade Gresham limped off in the final term with adductor tightness and North debutant Finnbar Maley missed a shot to snatch victory, with the Bombers claiming a 9.11 (65) to 9.8 (62) win at Marvel Stadium on Thursday night.
"The thing that I was really pleased with tonight was the resilience and the character of the group," Scott said.
"To North's credit, they were never out of it. We could never really put them away. They just kept coming.
"We obviously had some adversity in the last quarter, and coaches are always loath to individualise, but we had some individuals that just stood up in big moments, players that we just couldn't take off the ground."
Those clearly included the outstanding Bombers skipper Zach Merrett (35 disposals) and veteran ruckman Todd Goldstein.
Ridley, in his 100th game, limped off shortly before half-time.
Big man Jones was taken off on a stretcher after attempting to spoil a mark then landing awkwardly on his left ankle, which bent at an awful angle.
He was taken to hospital with, at minimum, a dislocated ankle.
Defender Jaxon Prior could come under scrutiny for a dangerous, slinging tackle on Cameron Zurhaar.
North defender Jackson Archer suffered a left hamstring injury in the second quarter and was substituted for Bailey Scott.
"He was limping pretty badly. I dare say it's not a slight strain. He'll miss some weeks, I'm sure," coach Alastair Clarkson said.
The match came a day after North put a media ban on pundit Kane Cornes for criticism of Harry Sheezel and Jy Simpkin that the club believed had crossed the line.
Sheezel (32 disposals) grew into the game while Simpkin (21) kicked two crucial goals when North needed him.
Ruckman Tristan Xerri (37 hitouts, 25 disposals) was dominant against former teammate Goldstein.
Essendon kicked the first three goals and six in the opening term.
The Kangaroos, down by 22 at half-time, found fresh intensity and capitalised on Ridley's absence down back, snagging the first four goals of the second half.
Zurhaar levelled the scores early in the fourth before Isaac Kako steadied Essendon.
Zane Duursma cut the lead back to three points, but Maley took too long to take his set shot, was called to play on, missed and Essendon held on.
"His humility would suggest he feels like he's let the team down but he hasn't let us down at all," Clarkson said of Maley.
"He's a ripper and he'll bounce back into the club on Monday and get himself ready for the next game.
"We came back from a game that looked shot for us at quarter-time and we found a way to get back into a contest."
North Melbourne, winless in six, next head to Hobart to face reigning premiers Brisbane in nine days, while Essendon (4-3) host Sydney next Saturday.
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