Steve McClaren's men arrived at Goodison Park on the back of three straight wins, but James Beattie's 16th-minute header ended that run and handed the Toffees their first home Premiership win of the campaign.
Boro created enough chances to have claimed at least a point but Yakubu Ayegbeni wasted the best of them early on, before Franck Queudrue planted a late header against the woodwork.
The visitors started strongly, with Gaizka Mendieta and Fabio Rochemback dominating midfield, and showed few signs of fatigue following their midweek UEFA Cup exertions against Dnipro.
However, Boro's failure to capitalise on their early possession proved costly when Everton won a corner from a rare attack.
Beattie, who showed signs of returning to the form that once made him an England striker, stole ahead of Ugo Ehiogu and placed a header beyond the stranded Mark Schwarzer.
Yakubu should have levelled almost immediately, but was unable to beat Nigel Martyn when put clean through on goal.
Beattie and Duncan Ferguson posed a formidable threat to the visiting defence and, as Everton began to take a grip on the game, the ex-Southampton man powered a header over the crossbar from a promising position.
After the break the home midfield, with Tim Cahill finally back to near his best, managed to snuff out Boro's attacking threat and restricted them to little more than half-chances, as Jimmy Floyd Hasselbaink fired wide and George Boateng high from the edge of the area.
David Moyes' men should have made sure of the points 10 minutes from time but Beattie somehow managed to find the woodwork when it looked easier to score.
That set-up a frantic finale, but the Goodison Park faithful were able to breathe a sigh of relief after Queudrue headed Boro's last clear chance against the bar and the ball bounced to safety.