Jonathan Stead's first goal of the season and Blackburn's fourth away win of the campaign damaged Everton's push for a Champions league place.
Stead, a 14th-minute substitute, struck a fizzing, low shot into the bottom corner on 71 minutes to boost his side's hopes of Premiership survival.
It was a deserved win for Blackburn, who had the better of a scruffy game with few clear-cut opportunities.
Marcus Bent had Everton's best chance but Brad Friedel saved at his feet.
Blackburn dominated the early exchanges, enjoying much more possession than their opponents but lacking the guile to take advantage.
They did penetrate Everton's resolute defence once but Paul Dickov was closed down quickly by Nigel Martyn, who smothered the shot.
Rovers' skipper had looked sharp but was forced off early on after taking a knock to the knee.
Everton have been notoriously slow starters in the Premiership at Goodison this season - they have yet to reach half-time in the lead.
And their rhythm was disrupted as they too were forced into a change.
Mikel Arteta twisted his ankle and Everton reshuffled from a 4-5-1 to a 4-4-2 formation, with Duncan Ferguson coming on to keep Bent company up front.
But the added attacking threat only mustered one clear opportunity to break the deadlock in the first half.
And in keeping with a scrappy match, Everton took route one to goal as Ferguson nodded on a high ball into the path of Bent.
But the striker was denied by the onrushing Friedel, who showed he was as alert as Martyn had been.
Lee Carsley tried his luck with two free-kicks but neither were on target.
As expected, Everton picked up the pace after the break and began an aerial bombardment.
But although Ferguson consistently rose above his markers, he could not direct his efforts accurately.
The lively David Thompson, who had caused problems with his busy style, volleyed wide as Blackburn interrupted Everton's newly-found dominance.
And just as the hosts may have felt they were starting to get a grip on the game, it all changed midway through the second half.
Steven Reid's through-ball split the Toffees' defence and Stead smashed a shot into the left corner from the right side of the box.
Leon Osman twice went close for Everton as they pushed for an equaliser.
But Blackburn benefited from good organisation and a determined approach to clinch the win.
Everton: Martyn, Hibbert, Weir, Yobo, Pistone (McFadden 76), Carsley, Osman, Cahill, Arteta (Ferguson 24), Kilbane, Bent. Subs Not Used: Wright, Stubbs, Plessis.
Booked: Weir, Carsley, Cahill.
Blackburn: Friedel, Neill, Todd, Nelsen, Johansson, Mokoena, Reid, Flitcroft, Thompson, Pedersen, Dickov (Stead 14). Subs Not Used: Enckelman, Short, Tugay, Gallagher.
Booked: Mokoena, Stead.
Goals: Stead 71.
Ref: P Dowd (Staffordshire).