Everton suffered an early scare when keeper Stefan Wessels needed treatment to a head wound after a clash with former Goodison striker Francis Jeffers, but the German carried on after having his injury bandaged.
And he was largely untroubled in a desperately poor first 45 minutes, with Jermaine Johnson off target with three long-range efforts for Wednesday.
Everton stepped up the pace after the interval and McFadden and Yakubu demonstrated why manager David Moyes left England striker Andrew Johnson on the bench.
Deon Burton wasted a good chance to bring Wednesday level, but he wasted the opportunity and the threat of McFadden and Yakubu proved too much for the Owls defence.
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