The Bombers overcame a sluggish start in which they trailed by one-point at half-time but ran over the Lions with nine goals to three in the second half to win 15.12 (102) to 9.12 (66).
It was their first victory at the Gabba since their last premiership year in 2000 where they got up 19.13 (127) to 9.9 (63).
The win moved Essendon into third position and stretched the Lions' winless start to the season to seven matches - and just three wins in their past 25 overall.
The Bombers were slow to get going, with Ashley McGrath kicking the match's first two goals, but a tidal wave of entries inside forward 50 eventually told against the home team.
Essendon won the forward 50 entries decisively in each quarter, 20-10 in the first, 19-7 in the second, 20-6 in the third and 16-13 in the fourth for an overall 75-36 advantage.
The Lions played with an open forward line and generated 13 scoring shots from their 17 first-half entries to lead by a point, while conversely the Bombers squandered their chances with five shots at goal going out on the full.
Things turned in the third quarter with two goals apiece to Jobe Watson - who was subbed late in the quarter with ice on his hamstring - and David Zaharakis, setting up a match-winning lead.
Zaharakis swung the match with 20 disposals and four goals in the second half as the Lions appeared to run out of legs against the competition's highest scoring team.
This was shown as Simon Black kicked the ball directly to Watson in his defensive 50 for a goal and Rohan Bewick handpassed straight into Tom Bellchambers for Zaharakis to another goal.
Bombers midfielder Heath Hocking may come under scrutiny from the match review panel for his first quarter hit on James Pokinghorne, which left the young Lion dazed and unable to return with concussion.
Essendon 3.2 6.6 10.10 15.12 (102)
Brisbane Lions 3.5 6.7 6.10 9.12 (66)
GOALS
Essendon: Zaharakis 4, Crameri 3, Monfries 2, Watson 2, Hille 2, Reimers 2
Brisbane Lions: McGrath 2, Bewick, Clark, Stiller, Drummond, Rich, Adcock, Rockliff.
BEST
Essendon: Zaharakis, Hille, Monfries, Hooker, Myers
Brisbane Lions: Adcock, Rich, Merrett, Leuenberger, Hanley
INJURIES
Essendon: Michael Hurley replaced in selected side by Travis Colyer, Henry Slattery replaced in selected side by Michael Hibberd
Brisbane Lions: James Polkinghorne (concussion)
SUBSTITUTES
Essendon: Watson replaced by Colyer late in the third quarter
Brisbane Lions: Polkinghorne replaced by Harwood at start of the second quarter
Reports: Nil
Umpires: Ritchie, Stevic, Kamolins
Official crowd: 24,921 at the Gabba