The west Londoners' second leg win at Craven Cottage came after a comfortable 3-1 success at Seaview and sets up a trip to Croatian side RNK Split next week.
Fulham were frustrated in the first half and Andrew Johnson's neat finish to a team move was the only goal to show for their barrage of attacks.
However, goals were much easier to come by after the restart as Damien Duff, Bobby Zamora and Steve Sidwell all netted to send the majority of the 15,767 supporters home happy.
Martin Jol sent out a strong-looking side as the Cottagers looked to secure safe passage into the third qualifying round, handing recent signing John Arne Riise his Fulham debut.
Crusaders made one change to the side that lost the first leg, with the Northern Irish team starting Ciaran Gargan in place of David McMaster.
Despite needing a huge swing to progress, Crusaders' substantial travelling support bellowed choruses of "We're going to win 3-0" from the offset.
The visitors went close to keeping their hopes alive in the third minute when Stuart Dallas found space to turn and send in a 20-yard shot that sailed just over the bar.
However, Fulham were controlling possession with ease and Johnson almost took advantage with a fizzing drive in the eighth minute.
The Cottagers continued to exert pressure without too much effort and converted that dominance into an opening goal with a slick team move in the 19th minute.
Riise squared a cross from the left flank and Zamora's step-over gave Johnson the opportunity to jink wide of his marker and strike low into the bottom left corner.
The home faithful thought Sidwell had doubled Fulham's advantage five minutes later, but his neat flick from Johnson's cross had only rippled the side-netting.
Zamora's stooping header tested goalkeeper Sean O'Neill as the home side continued to press, before Crusaders had a chance of their own.
Gargan broke free down the left wing and Timmy Adamson nudged his cross just over the bar after getting ahead of Brede Hangeland in the six-yard box.
It proved to be a mere respite for Crusaders, who were forced to defend for the remainder of the half.
Sidwell went closest to netting another first-half goal, shooting just wide after a superb team move cut through the middle of the Crusaders team.
Fulham continued in the same vein after the break and only a point-blank save from O'Neill prevented Sidwell nodding home Duff's free-kick.
Sidwell was proving a real thorn in Crusaders' side and came a whisker away from netting with a 52nd-minute back-post header that nicked the post before going wide.
However, Duff soon ended any remaining hopes the Northern Irish side had of progression by shooting across goalkeeper O'Neill from a tight angle after latching on to a great ball from Philippe Senderos.
Fulham netted a third goal in the 66th minute after another slick team move, with Duff stepping over Johnson's left-wing cross for Zamora to finish with gusto.
And the west Londoners' advantage was increased further four minutes later as Sidwell belatedly netted, heading home Duff's corner.
Jol made wholesale changes after the fourth goal and substitute Bjorn Helge Riise almost made the ideal impact, although his fierce shot went just wide.
The effort was the last moment of note as the game petered out, as Fulham secured a clean sheet and progression to the third qualifying round.