Manchester United reject Diego Forlan showed his intent early on for Villarreal with a forward run that was blocked by Alessandro Pistone.
Everton replied instantly at the other end only for Tim Cahill to be knocked disappointingly off the ball.
Everton were determined to set the tempo but the fussy referee pulled up Cahill for an innocuous challenge on Juan Riquelme.
Simon Davies then played Pistone in on the left but his cross caught James Beattie on his left foot and Mariano Barbosa collected easily.
Mikel Arteta then swung in a lovely corner only for Cahill's decent header across goal to be parried.
Josico broke down an Everton move when he dispossessed Cahill but the home side were looking lively in the opening stages.
As Forlan tried to get into the game he unleashed a 35-yard screamer that flew high over Nigel Martyn's crossbar.
Following a Beattie free-kick, Arteta curled in a corner only for the referee to blow for a foul on Barbosa who made a meal of the challenge.
Forlan received a yellow card after a cynical challenge on Everton new boy Phil Neville.
Luciano Figueroa broke the deadlock on 27 minutes when he collected a pass and slotted home right footed from 15 yards into Martyn's far corner.
When Everton tried to hit back Cahill headed narrowly over on 34 minutes after good work by Arteta.
Beattie announced his arrival on the European scene when he met a beautiful cross by new boy Neville with his right foot and poked it past a despairing Barbosa.
On the stroke of half time though Josico restorred Villarreal's lead when he bulleted Sorin's cross home.
At the start of the second half Everton piled on the pressure but they couldn't break down a resolute Spanish defence. They nearly equalised in the 52nd minute but Kevin Kilbane's first touch was too heavy and Barbosa got to the ball first.
Villarreal were looking much more relaxed and it was no surprise when David Moyes introduced Duncan Ferguson and Marcus Bent for Kilbane and Beattie.
Ferguson almost scored a dramatic equaliser with his first touch and Bent nearly scrambled the ball home a minute later.
Arteta floated in a wicked ball which Barbosa punched but he also caught Cahill, who was left prone on the floor.
Everton replaced a poor Pistone with young Scot James McFadden with ten minutes remaining to no avail.
For all Everton's hard work the result was just about fair as Villarreal looked comfortable throughout and the home side lacked the cutting edge that teams need to progress in this competition.