The pair have made a stuttering start to the season with a return of one goal apiece before their trip to Hillsborough.
But the scoreline flattered the Premier League outfit as they struggled for most of the night to overcome brave Wednesday, currently bottom of the Championship and until five days ago without a point.
David Moyes might have singled out the Carling Cup as a realistic target for his team, but his side made heavy weather of overcoming the Yorkshire strugglers.
Scotland international McFadden grabbed the opener with a cool finish after 59 minutes after Yukubu picked him out with a pinpoint angled pass from the right.
But then two goals in as many minutes put Everton in the comfort zone and killed off Wednesday.
After 83 minutes a super cross from the right from substitute Phil Neville was headed past the helpless Lee Grant by McFadden and within a minute he picked out his strike partner Yakubu, who lashed in a low shot.
Ex-Everton teenage prodigy Francis Jeffers, whose goal at the weekend gave Championship bottom club Wednesday their first points of the season, was on fire as he tried to put one over his former side.
The last time Everton were at Hillsborough Jeffers was a 17-year-old striking sensation for the Merseyside outfit at the start of his chequered career.
Eight years on he was drawing the boos from Everton fans and cheers from home supporters as he rattled the top-flight outfit.
He came close to a scoring connection in the first minute after Marcus Tudgay headed down a Wade Small cross, but Everton keeper Stefan Wessels made a brave block that cost him a head injury and left him with it heavily bandaged.
Jeffers was the creator after nine minutes slipping a neat ball for Graham Kavanagh who tore through and forced Wessels to save after two attempts with his blistering long-range strike.
Another break from Jermaine Johnson had Everton backing off but he fired a 25-yarder wide before producing a mishit shot that Jeffers almost reached.
Everton boss Moyes was fuming after Sunday's defeat at Aston Villa but his mood was not improved by his side's inept opening.
He made five changes from the weekend and gave record signing Yakubu a chance to add to his solitary goal, picked up ten minutes into his debut against Bolton.
But he Nigerian playing alongside McFadden had to play second fiddle to Wednesday's young centre-back Richard Wood.
And England striker Andy Johnson, desperate to end his miserable goalless run stretching back to March, had to watch from the bench as Everton struggled to warm up 2,500 fans who made the trans-Pennine trip.
In added time Everton defender Tony Hibbert was fortunate to escape a second yellow card when he made a lunging tackle on Small but remained unpunished by referee Rob Styles.