The Dockers won the opening seven clearances of the third quarter and kicked three of the opening four goals of the term to draw within eight points.
Jayden Laverde steadied after some nice build up play from Anthony McDonald-Tipungwuti and Heath Hocking.
When Zach Merrett kicked his third of the match a minute later, the half time margin of 20 points was restored.
James Stewart added a third goal, before Merrett kicked his fourth of the game to cap a four-minute burst that yielded four goals and a 32-point lead for the Bombers.
Hocking added a fifth for the quarter to extend the margin to 38 points.
The five-goal run was built on a midfield that got on top of their Fremantle counterparts. Tom Bellchambers was instrumental in the middle of the ground and the players at his feet made the most of the service.
At the final change the margin was 32 points.
The Dockers kicked the opening three goals of the last quarter to cut the margin to 14 points with 15 minutes remaining.
When Hayden Ballantyne kicked the visitors fourth of the term, Essendon's lead was just eight points.
Hocking found the answering goal with ten minutes remaining. But the Dockers didn't relent. With eight minutes to play, the margin was ten points.
Stewart's fourth goal of the match got the Bombers out to a 16 point lead.
From there, the Bombers did enough to secure the win.