Leon Osman scored a goal in each half to secure victory and fifth place in the Premier League for Everton.
After Louis Saha hit the bar with an early header, he struck first on the stroke of half-time by rounding keeper Mark Schwarzer and sliding home.
And midfielder Osman made it 2-0 late on with a curling 20-yard strike.
Fulham's Clint Dempsey had a shot cleared off the line but they stayed seventh despite the loss and will play in the Europa League next season.
A trip onto the continent for Roy Hodgson's side was guaranteed when rivals Tottenham lost 3-1 at Liverpool.
Hodgson happy with seventh-place
Everton deserved their half-time lead having just about shaded an entertaining first period after Saha hit the crossbar following Osman's good work down the right flank.
Promising young midfielder Jack Rodwell tested Schwarzer with a low 20-yard drive and there were further efforts from Tim Cahill and Steven Pienaar to keep the Fulham keeper on his toes.
At the other end Zoltan Gera should have done better with a free header at the back post but headed straight at Tim Howard but moments later the Hungarian sent a thunderous effort just over the bar from 25 yards.
Although Fulham enjoyed their fair share of possession in the searing heat at Craven Cottage, without both Andy Johnson and Bobby Zamara, they lacked a real threat up front - and it was always Everton who looked the more likely to break the deadlock.
Saha had a fierce shot tipped round the post but on the stroke of half-time, the visitors went ahead when the brilliant Pienaar found Osman, who intelligently lost his marker and beat the offside trap before taking the ball around Schwarzer and coolly tapping home it into an empty net.
Everton went close to increasing their lead as Schwarzer did well to tip Saha's close-range header around the post.
John Pantsil then shot wide from 18 yards for Fulham, who finally sent on striker Zamora as they went in search of an equaliser. He had a golden opportunity to level with only minutes remaining, but fired his left-foot half-volley at the legs of Howard.
The miss proved costly as Everton went further ahead moments later as Osman picked the ball up outside the box, dinked it past two Fulham defenders and curled a left-footed shot past Schwarzer and into the back of the net.
Fulham kept going despite the setback and only Tony Hibbert's last-ditch clearance denied Dempsey a goal, but they had the consolation of their highest finish in 20 years of top-flight football.
Fulham manager Roy Hodgson: "We've exceeded everyone's expectations and it's amazing how things can turnaround.
"We were hoping we'd secure seventh spot in style, but it wasn't to be.
"But Liverpool did the job against Tottenham and I think over the 38 games we deserve to be seventh and that will do me very nicely.
"The players deserve a lot of credit as they have worked very hard."
Everton manager David Moyes: "The display and the result was excellent.
"This is always a hard place for Everton to come and credit to Fulham for how they done this season.
"The first goal was crucial. I thought we deserved to be leading at the break and it was a well taken goal. I'm pleased with the points and to finish fifth."
BBC Sport Player Rater man of the match: Everton's Steven Pienaar 9.86 (on 90 minutes).
• Please note that you can still give the players marks out of 10 on BBC Sport's Player Rater after the match has finished.
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