Needing a win to stay ahead of Richmond and hold onto eighth spot, the Bombers started nervously and trailed by seven points at quarter-time.
The sides traded blows in the second term, Essendon briefly hitting the front after Sam Heavyside expertly roved a pack and snapped truly.
But the Blues answered straight back through Zach Ballard and reclaimed the lead when American big man Matthew Korcheck goaled.
Bombers on-baller Aaron Heppell had the final say for the half, bouncing through a classy goal to level the scores at 42 apiece at the main break.
It was all Essendon in the opening minutes of the third quarter, Will Hams making the Blues pay after they coughed up a 50m penalty.
Shaun Edwards stretched the margin to 14 but Northern hit back again through Glenn Strachan to stay in touch.
Only seven points separated the teams when Harry McKay missed at the 24-minute mark, with little sign of what was about to come.
Ryan Crowley slipped a Billy Gowers tackle two minutes later and opened the floodgates.