But Fellaini again found England full-back Baines and another inviting cross was flicked in by Beckford.
Fellaini had been set to visit the specialist last week before his train to London was cancelled.
However, some observers contended that Fellaini was equally at fault, with television replays suggesting he connected with Kyrgiakos's shin.
Marouane Fellaini headed over in a poor first half before Steven Pienaar's shot was well saved as Everton pressed.
And it would appear Everton will likewise have to plan without Fellaini at least until the start of next season.
On the half-hour mark Ladislav Onofrej had a penalty shout correctly rejected after he was cleanly challenged by Marouane Fellaini.
Marouane Fellaini headed home the opener in the 42nd minute before Steven Pienaar doubled the lead in the 59th minute.
Marouane Fellaini gave Everton the lead when he slotted in Leighton Baines' cross before Tim Cahill headed in Steven Pienaar's corner.
The Toffees, without their top scorer Tim Cahill, relied on Saha, Rodwell, Marouane Fellaini and Diniyar Bilyaletdinov to provide the bullets.
He had played a starring role, Marouane Fellaini had been outstanding and Tim Cahill had put in his best performance in weeks.
Everton also had an appeal for a penalty turned down when Fellaini fell, and Kevin Mirallas had an effort ruled out for offside.
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When Aimar played a short ball to Di Maria, Marouane Fellaini dawdled in defence and another smart cross proved easy pickings for Cardozo.
Pompey's Aruna Dindane saw his strike saved by Everton goalkeeper Tim Howard before Marouane Fellaini's close-range header was kept out by James' foot.
Osman, Marouane Fellaini and Phil Neville got to grips with the midfield and allowed Everton to dominate possession and territory from the outset.
After Dagnall spurned his opportunity Everton seemed certain to go further ahead, with Fellaini firing over after a neat exchange of passes with Beckford.
Fellaini had the first chance after a delightful first-time pass from Tim Cahill, but the big-haired Belgian's poked effort was brilliantly blocked by Ruddy.
Boro led 1-0 at half-time through David Wheater's 44th-minute goal but Marouane Fellaini and Louis Saha scored to give Everton a showdown against Manchester United.
Yet the Toffees were made to pay a high price when the statuesque Marouane Fellaini catastrophically slipped outside his own penalty area in the seventh minute.
Baines unleashed a fierce right-footed drive that Cech could only parry and Fellaini tapped home, but he was ruled offside and replays suggested the decision was correct.
Holt's contribution - his seventh goal in 14 league games this season - could have ended soon after when he appeared to elbow Fellaini in the jaw.
But it was not an advantage they were to hold for long, despite the efforts of the tenacious Marouane Fellaini, who did his best to repel the Gunners.
Fellaini, along with impressive fellow-midfielder Jack Rodwell, was beginning to have a greater influence on proceedings but it was Osman and Pienaar who combined to put Everton ahead.
Marouanne Fellaini put David Moyes' team ahead in the 33 minute before Carlos Tevez equalized from the penalty spot 10 minutes later after Edin Dzeko had been brought down.
Louis Saha has been plagued by hamstring trouble which has restricted him to 14 matches this season, while midfielder Marouane Fellaini is playing with a cracked bone in his back.
When fleeting opportunities did fall the home side's way, Fellaini headed over and a Jack Rodwell nod towards goal was diverted above his own goal by Wigan midfielder Ben Watson.
The hosts went ahead with a thumping drive from Dmitri Likhtarovich but Marouane Fellaini drew Everton level from a Leighton Baines free-kick and Tim Cahill won it with 13 minutes remaining.
Moyes even claimed that Fellaini was the best midfield player in the country based on current form following his starring role in Everton's 2-0 home defeat of Manchester City last month.
Paul Lambert's Villa had been 3-1 up against Everton at Goodison Park, before two goals from Marouane Fellaini -- the second in injury time -- rescued a point for the Toffees.
With three minutes left, Carroll rose into the London sky with big-bodied opponent Marouane Fellaini all over him, met Craig Bellamy's free kick and headed it past Everton goalkeeper Tim Howard.
Two minutes later Everton were ahead when Baines picked out the distinctive mop-haired figure of Fellaini with a low ball from the left leaving the Belgian with a tap-in at the far post.
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