Steve Kean's men continue their good run of form at Goodison Park, after falling behind to a controversial opening goal with Fellaini hand balling in the build-up
Tim Cahill scored his first goal in over a year to give the Toffees the lead in controversial circumstances before David Goodwillie bundled home an equalizer in the second half.
Everton manager David Moyes made just one change to his side, bringing Victor Anichebe in for Royston Drenthe. At the back Shane Duffy continued to deputize for the injured Sylvain Distin.
Steve Kean was able to bring Scott Dann back into the Blackburn defense and was forced to bring David Goodwillie in for the suspended Yakubu.
The home side had a good chance to take an early lead as Phil Neville, on his 35th birthday, sent Landon Donovan away down the right flank and the American crossed for Victor Anichebe but the burly striker could only scuff an effort wide.
On the other end, David Dunn had two good chances after being set up by Junior Hoilett and then Morten Gamst Pedersen, but was denied by Howard on both occasions, though Dann hit the crossbar soon after.
The Goodison Park crowd was infuriated as Radosav Petrovic looked to catch Louis Saha in the throat with an elbow, nothing was given by referee Mark Halsey but the home fans soon had better things to shout about.
Rovers failed to clear a corner and the ball was worked back to Landon Donovan, with the American's chipped ball was headed goalwards by Fellaini and after Paul Robinson's save the Belgian blatantly handled the ball into Cahill's path and the Australian slammed home his first goal since a strike against Manchester City in December 2010.
Everton was spurred on by the goal, as Neville found Cahill down the right and the Australian's delightful reverse ball found Donovan in the box, but the LA Galaxy loanee could only screw his shot wide.
Rovers hit back and came close to an equalizer as Goodwillie's shot was blocked into the path of David Dunn who swept the ball past Howard but could only look on in agony as his effort hit the post and was cleared.
Anichebe's power and Donovan's pace were dangerous on the counter for the Toffees and Petrovic picked up a booking for fouling the American as he looked to burst clear, though Leighton Baines sent the resulting free kick curling wide.
Both sides continued to work hard in the driving rain at Goodison Park but lacked the cutting edge to create clear chances and went in for the half with Everton holding a controversial lead.
A scrappy start to the second half saw both teams struggle to create many chances, as a wayward long distance effort from Cahill summed up both side's play, Moyes also made a change to his side, bringing Drenthe on for the anonymous Louis Saha with barely 10 minutes gone in the second period.
The game continued at a stop-start pace with Goodwillie being too isolated to make a difference for Rovers, who replaced Dunn with Mauro Formica on the hour.
Petrovic then flashed a 30-yard effort wide of Howard's far post before Pedersen hit an atrocious effort into the stands from a similar distance following a good run by Hoilett.
Drenthe worried the Blackburn backline with his pace and did magnificently to take on Martin Olsson down the right and flash a ball across the face of goal with no Everton teammates well-placed to turn it home.
Blackburn was looking to its own fleet-of-foot wide man, Hoilett, to inspire a comeback, as the Canadian drew a foul out of Darron Gibson which saw the former Manchester United midfielder booked.
The resulting free kick drifted into the box and though Howard missed it, Cahill was well placed on the line but he could only hit his clearance at Goodwillie, who deflected the ball home for a bizarre Rovers equalizer.
With time drawing to a close and both sides remaining unable to unlock each other's defenses, Moyes sent on Apostolos Vellios for Victor Anichebe hoping the Greek forward would be able to add to his three goals scored from substitute appearances this season.
The Toffees went close soon after, as Baines' superb set piece delivery was met by Shane Duffy who could only thunder his header onto the crossbar.
Denis Stracqualursi replaced Gibson with just three minutes remaining as Everton pushed forward for a late winner.
Marouane Fellaini saw his header well saved by Robinson and from the resulting corner, Jason Lowe did excellently to clear off the the line after Cahill's effort to preserve a point for Steve Kean's men.