Club Brugge's hopes of reaching the quarter finals were quashed by half time after Rafa Silva's opener was followed by a delightful Goncalo Ramos finish.
With their opponents down and out, Benfica added a third in the 56th minute when Ramos met Alex Grimaldo's squared ball, guiding home his second goal of the game.
Joao Mario dispatched his spot kick to continue the rout, before substitute David Neres put his name on the scoresheet in the 77th minute.
Bjorn Meijer produced a late consolation goal for the visitors, but it did little to dampen the mood of the home faithful.
As a result of their dominant display, Benfica progress to the Champions League quarter finals for the second straight season.
After claiming a 2-0 victory when they travelled to Belgium three weeks ago, Benfica entered the second leg in a promising position.
Instead of protecting their two-goal lead, it was clear from the first whistle that the Portuguese champions were determined to add to their tally.
The majority of those in attendance at the Estadio da Luz were celebrating within two minutes when Mario flicked the ball past Simon Mignolet, but those celebrations were short-lived, as the goal was swiftly chalked off for offside against Ramos in the build-up.
The Belgian side continued to live dangerously, though, with Brandon Mechele blocking Mario's effort on the goalline to keep the hosts at bay.
After soaking up the early Benfica pressure, Club Brugge attempted to halve the aggregate deficit, but Hans Vanaken was unable to direct his tame header on goal.
Benfica quickly wrestled back control, and their persistence finally paid off when Silva opened the scoring in the 38th minute.
Ramos drove purposely down the left flank before cutting inside to pick out Silva, who moved away from a couple of defenders to find the net with an exquisite finish from the outside of his right boot.
After setting up the opening goal, Ramos put his own name on the scoresheet in first-half stoppage time to end any lingering hopes of a Club Brugge comeback.
The 21-year-old wriggled away from one defender after another, before thumping the ball into the bottom corner.
Benfica showed little mercy in the second period, as Ramos grabbed his second goal in the 57th minute, sweeping home from Grimaldo's low pass.
The visitors' miserable evening was compounded when the referee pointed to the spot after Abakar Sylla brought down Gilberto in the box.
Mario assumed responsibility for the resulting penalty and kept his composure to send the goalkeeper the wrong way.
With just over 10 minutes remaining, Neres rounded off a slick passing move, driving the ball past a helpless Mignolet to take Benfica's tally to five.
There was still time left for Meijer to find a consolation goal, but his thunderous effort could not prevent Club Brugge's European campaign from ending with a whimper.
The Portuguese giants have now recorded five consecutive victories across all competitions, while Scott Parker has won only one of his 12 games in charge.