Midfield maestro Mikel Arteta returned after recovering from his ankle injury while James McFadden replaced the crocked Andy Johnson in attack. Tim Howard also returned after his hand injury.
Boro, for their part, welcomed back Egyptian striker Mido, Jonathan Woodgate and Gary O'Neil after their disappointing Carling Cup exit at the hands of Spurs in midweek.
It was Middlesbrough who started brightest and should have gone ahead when George Boateng was given far too much space to run in on goal, but somehow the midfielder directed his effort wide with Howard stranded off his line.
It was Everton though who went ahead after seven minutes, after Yakubu's back header from an Arteta corner saw Woodgate only half clear into the air for Joleon Lescott to head back in for his third Premiership goal of the season.
It was end to end stuff for the next 30 minutes with Stewart Downing proving a real handful for Tony Hibbert to contain, but it was Everton's Yakubu who should have scored against his former club, but he headed a relatively easy chance way over the bar.
Boro's Lee Dong-Gook missed an absolute sitter on 26 minutes as he headed against the bar with the goal at his mercy, after rising impressively with Everton's defence in disarray.
O' Neil was lucky to stay on the pitch as the normally officious Mike Riley deemed his horrendous tackle on Steven Pienaar was only worthy of a yellow card.
Seconds later, the defender shoved Arteta of the ball so viciously the Spaniard ended up on his back, nearly crashing into the advertising hoardings. Referee Riley bizarrely waved play on.
Minutes before the break, Pienaar could have doubled his side's lead after great work by Arteta saw Hibbert free to provide a telling cross, which the diminutive South African could only head at Mark Schwarzer.
Everton finished the half strongly as they impressed their intentions on a Boro side full off steam but little guile.
The home side killed the game on 58 minutes as a Boro move broke down in midfield and Everton capitalised with the move of the game.
McFadden picked the ball up and passed to Pienaar, who deftly clipped the ball off the back of his heel to Arteta who was passing him to run wide.
Arteta then provided a neat pass to Pienaar, who had carried on his run into the penalty box and slid the ball home inside the far post.
Boro continued trying to counter, but Everton looked to have the measure of them by this time and it was the home side who could have gone further ahead in the closing stages.