Kick-starting his Premier League career with a win, Paul Ince's side looked the better team as David Moyes was forced to pick from a squad that had ten senior players missing.
The first half was totally dominated by the visitors and the Toffees found themselves lucky to be going in at the break with a score of one goal a piece.
But the half-time break turned things around for the home side in a match that could have gone either way.
Having not brought any new faces to Goodison over the summer, the Blues boss was forced into playing 17-year-old Jack Rodwell in the middle of the park and only one striker in Yakubu up front.
Making his first league start, Rodwell found a bit of space after four minutes on the edge of the box, but his low drive was easily smothered by Paul Robinson in the Blackburn goal.
That was the last shot on goal for the home team for over 30 minutes as Ince's men piled on the pressure.
A high ball crossed into the box by right winger Steven Reid on seven minutes found the head of tall striker Roque Santa Cruz but, after holding off a challenge of Joseph Yobo, the Paraguay international could only put the ball wide of Tim Howard's goal.
Another looping cross into a packed 18-yard box by Reid could only be headed over the bar once again by the powerful Santa Cruz.
With an effort by David Dunn and a blocked shot by Morten Gamst Pedersen, it was only a matter of time before the visitors broke the deadlock and they did so on 22 minutes.
A pass from Pedersen across the edge of the box to Dunn, who faked a right-foot shot sending Phil Jagielka sliding past, then shifting to his left, the midfielder curled the ball from 20 yards past the outstretched arm of Howard.
Having been outplayed for nearly 45 minutes, Everton found themselves deep inside the opponents half with only stoppage time to play and an attempted cross from Mikel Arteta hit the hand of Reid resulting in free-kick wide left of the 18-yard box.
Putting the ball down, Arteta caught Robinson napping and drilled home a shot inside the former England number one's near post.
The Blues came out a different side in the second half and the game became an end-to-end contest that could have gone either way.
A Leighton Baines cross in the first three minutes fizzed across the box and missed both Yakubu and an on rushing Leon Osman by a matter of inches.
Everton took the lead on 64 minutes with a well worked goal from Yakubu, who started the move inside his own half.
His pass released Arteta down the left and a deep cross to the back post found the Nigerian out jumping Stephen Warnock to nod home his first of the season.
The lead lasted two minutes as Warnock made up for his slack defending by sending a 30-yard pass to an onside Santa Cruz, who brought the ball down, leaving Joleon Lescott screaming for offside, and slotted it easily past Howard.
David Moyes brought on Everton's youngest ever first-team player in Jose Baxter - who is 16 years and 196 days old breaking James Vaughan's record by 75 days - and the youngster could have won the game in the final minute.
A deep cross from Jagielka found the head of Baxter on the back post, but the England Under-17 star couldn't keep it down.
With the last kick of the game, Blackburn gave their manager the perfect start to his Premier League career after a needless free-kick was given away by Yakubu which gave Warnock the chance to put the ball in the box.
His cross found Ryan Nelsen who headed the ball against the post and rebounded straight to an on rushing Andre Ooijer, who easily slotted home to steal all three points.