Harry Wilson was Brentford's nightmare again as Fulham scored twice in just two minutes to stage a comeback to win 3-2 at the Gtech Community Stadium.
Wilson scored a stoppage-time brace in the return leg in November to give the Cottagers victory, and his 70th-minute goal, just after Tom Cairney had equalised, proved decisive.
Raul Jimenez opened the scoring for the visitors before Bryan Mbeumo, who missed a first-half penalty, and Yoane Wissa scored their 19th goals of the season.
Cairney, who has yet to be offered a new contract at Craven Cottage with his deal expiring in the summer, equalised before substitute Wilson repeated the feat.
Both teams have been battling for eighth place and a place in the Conference League in recent weeks, but those hopes were dashed after Crystal Palace's FA Cup victory on Saturday meant it was the Eagles who will be heading into Europe next season.
Vissa wasted a glorious chance when he found himself one-on-one with the defence moments before Fulham opened the scoring in the 16th minute.
Adama Traore, whose contract at Craven Cottage was extended by a year this week, crossed accurately and Jimenez headed the ball past Mark Flecken.
The fans were very supportive of the teams in a tense encounter where both sides chose to play hard, but it was Brentford who equalised in the 22nd minute shortly after Jimenez's goal.
Traore turned from hero to villain when he was robbed in midfield and Vissa linked up with attacking partner Mbeumo on the right flank before the latter fired his weak right foot into the bottom left corner.
Minutes later, Joachim Andersen brought down Kevin Schade in the penalty area, but Mbeumo was unable to convert the resulting penalty, which was saved by Bernd Leno.
However, Brentford's persistence was eventually rewarded as their physical advantage told from a set piece.
Fulham failed to cope with a long throw and Bees captain Christian Norgaard found himself at the far post where he flicked the ball over Leno's arms before Wissa tapped it home.
Fulham equalised in the 68th minute through substitute Cairney, who headed home from close range.
Two minutes after Fulham had equalised, chants of “Shoot!” echoed across the Gtech Community Stadium from away fans as Wilson fired home from long range, leaving Flekken frozen in his tracks.
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