Laurie Sanchez brought his Fulham side to Goodison looking for a first away win in 25 games but he found no quarter given by an Everton side that came to life in the second 45 minutes.
Fulham started brightly on a wet, windy and frankly miserable Saturday afternoon. Steven Davis forced a punched clearance from Tim Howard in just the third minute.
As Everton regained their composure, Joleon Lescott almost put the hosts ahead from a Mikel Arteta free-kick which was well held by Fulham keeper Antti Niemi.
In fairness, the horrendous conditions on Merseyside made it difficult for either side to play with any degree of skill.
In fact, the most notable incident of the first half was a fine Niemi tip-over after an Arteta free-kick deflected off Davis' head.
At the end of the first half Fulham had probably shaded the game in the wet conditions.
Even the most optimistic Evertonian could not have predicted what was to come after the break.
Both teams came out for the second half unchanged, but Everton came flying out the traps, whatever David Moyes said at half-time clearly worked.
Everton's opening goal came when Yakubu toe-poked home after Niemi had parried a fantastic low volley from Tim Cahill straight to the big man's feet.
Two minutes later Danny Murphy forced a great save from Howard after he hit a rasping drive from outside the area, a shot which was Fulham's last meaningful effort on goal.
Ten minutes later Yakubu made it two after Spanish winger Arteta whipped in a dangerous corner, which found Phil Jagielka, whose smart back header fell to Yakubu.
The clinical forward made no mistake after directing his own header into the top left hand corner.
The Nigerian should have had his hat-trick after the best move of the game, which saw Steven Pienaar play a lovely one-two with Phil Neville and run almost the full length of the pitch to play in Yakubu, who then tried to slide in Arteta when a shot was the better option.
It was Pienaar who was instrumental in finally helping Yakubu complete his treble after the South African winger picked up the ball in the Fulham half, played it to Yakubu, received it back, and instead of playing it out to Arteta, cut it back intelligently into the big man's path, who evaded a last-ditch challenge to slot home.
The Nigerian left the field to a standing ovation before referee Steve Bennett blew the final whistle.