The 14.16 (100) to 12.7 (79) loss was the Bombers' third in a row to the Kangaroos, with the red and black's last win coming against the Kangaroos in round 16, 2001 at the MCG - a match rated as one of the best of the modern era.
The Bombers conceded eight of the last nine goals of the match with skipper James Hird unable to get into the contest to produce the kind of rescue act the Essendon faithful are accustomed to.
First-year Bomber Justin Murphy was outstanding with five goals, 27 touches and 10 marks, while Adam McPhee with three goals and Jason Johnson with 28 possessions were the best for the Dons.
A menacing Bombers coach Kevin Sheedy branded his side's performance as 'soft' after the match.
"(It was) an extremely disappointing loss. It's probably the softest loss I've seen (by) Essendon in a long time."
"On tonight's performance you'd have to say we need to have a look at ourselves and a look at the list of players and see if they really have the hunger to go on.
"And if they don't, we'll keep putting young players in till they do. We've been through that umpteen times before."
Saverio Rocca continued his fine recent form with five goals while Shannon Grant booted three goals and racked up 22 disposals for the Kangaroos.
Brady Rawlings, Daniel Wells and Michael Firrito were also good performers, while Shannon Watt, Glenn Archer and Leigh Colbert showed out in defence.
Rawlings and Archer switched between manning up on Hird, who was held to just seven touches for the night - a rare sight - while Watt held Matthew Lloyd to just one goal.
Essendon started the match in great style and dominated play early on, booting the first three goals of the match to lead by 17 points.
Brent Harvey opened the Kangaroos account at the 13-minute mark and by quarter-time the Roos were within one goal thanks to late conversions from Rocca and David King.
The Kangaroos hit the lead at the seven-minute mark of the second term when Rocca posted his second, but two in a row from Murphy put the Bombers back in front by 11 points.
Rocca bobbed up with his third mid-way through the term, but a brilliant goal in the pocket from McPhee again gave the Bombers an 11-point lead.
But the persistent Kangaroos kept challenging and when Grant kicked truly just before the main break Essendon led by just five points at half-time.
Murphy was instrumental in the third term with three majors as the Bombers piled on four unanswered goals to lead by 25 points at the 17-minute mark which was their greatest margin of the match.
The loss of Rocca with an injured ankle during this period, combined with the Roos poor kicking for goal was crucial, as the Shinboners registered six behinds for the quarter.
But the Kangaroos finally converted at the 21-minute mark via Grant and when Rocca, who was back on the ground, kicked his fourth just before three quarter-time, the Bombers led by just six points at the final change.
Overall, the Kangaroos had four more scoring shots in the third term as they posted 3.6 to Essendon's 4.1.
With the final quarter looming as a nail-biter, the Kangaroos made sure it would start that way, as Corey Jones kicked his first to give his side a one-point buffer - the Roos first lead since early in the second term.
McPhee answered with his third to regain the lead for the Dons at the seven-minute mark, but when Grant hit-back it was the Roos again by just the narrowest of margins.
Grant's third started was the start of four consecutive goals for the Roos and when Rocca booted his fifth at the 24-minute mark, the contest was all but over.
Essendon: 4.3 7.5 11.6 12.7 (79)
Kangaroos: 3.3 6.6 9.12 14.16 (100)
Goals: Essendon: Murphy 5, McPhee 3, Dyson, Fletcher, Lloyd, Richards
Kangaroos: Rocca 5, Grant 3, B.Harvey 2, Harding, Co.Jones, King, Motlop
Best: Essendon: Murphy, McPhee, J.Johnson, Fletcher, Bolton
Kangaroos: Grant, Rocca, Rawlings, Wells, Firrito, Watt, Archer, Simpson, Colbert
Injuries: Essendon: Richards (mild concussion)
Kangaroos: Nil
Reports: Essendon Nil
Umpires: Kennedy, Margetts, Goldspink
Crowd: 49,419
