Dickson Etuhu broke the deadlock for Fulham after 57 minutes
Andy Johnson's brace helped Fulham seal a commanding win in their first European tie for more than six years.
Roy Hodgson's side join Everton and Aston Villa in Friday's draw for the Europa League play-off round.
Leading 3-0 on aggregate, they dominated the second leg against Lithuanian side Vetra.
They had to wait until the 57th minute for Dickson Etuhu to break the deadlock with a header before Johnson added a quick-fire double from close range.
Joining Fulham in the battle for places in the group stage will be the likes of Roma, PSV, Galatasaray and Hamburg, as well as all the teams who lost in the third round of qualifying for the Champions League.
But Fulham have every reason to await that draw with optimism after a professional display on Thursday, albeit against limited opponents.
Having all but sealed their place in the next round with a 3-0 win in Lithuania, they made an understandably cautious start in torrential rain in west London.
Indeed, they might even have fallen behind in the 12th minute when Tomas Razanauskas unleashed a testing drive, which Mark Schwarzer did well to tip over.
But that was the closest the visitors came to a goal, while Fulham should have scored more than their three.
Johnson's looping header hit the woodwork and from the follow-up, Zoltan Gera's rifled shot was headed off the line by Gediminas Paulauskas.
Paul Konchesky, a constant threat down the left, flashed a shot wide and Clint Dempsey blazed over wastefully as the hosts failed to make their first-half dominance count.
But 12 minutes into the second half, Etuhu gave his side a deserved lead, making a clever run in the box to meet Konchesky's corner with an angled header into the far corner.
Johnson made it 2-0 when he got in front of his marker to convert Dempsey's cross.
With his side in complete control, Hodgson gave new signing Bjorn Helge Riise his home debut.
But it was fellow substitute Eddie Johnson who made the bigger impact, picking out his namesake Andy for an easy tap-in in front of goal.
Fulham: Schwarzer, Pantsil (Kelly 78), Hughes, Hangeland, Konchesky, Dempsey, Etuhu, Murphy, Gera (Riise 78), Zamora (Eddie Johnson 82), Andrew Johnson. Subs Not Used: Stockdale, Baird, Seol, Nevland.
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