David Villa scored twice but missed a penalty as pre-tournament favourites Spain wasted several clear-cut chances.
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David Villa's 20-yard free-kick took a slight deflection as it defeated Toldo for Valencia's second goal.
David Villa slotted home a penalty on the stroke of half-time after Steven Whittaker was punished for handball.
David Villa, Santi Cazorla, Marcos Senna also scored for Spain, but Dani Guiza had his effort saved by Buffon.
Spain dominated possession and could have scored more than the two goals they got through David Villa and Fernando Llorente.
Striker Fernando Torres has struggled to regain his form after knee surgery, leaving five-goal David Villa to shoulder attacking responsibilities.
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Despite the vast outgoings, Real have also been linked with Liverpool's Xabi Alonso, Valencia's David Villa and Bayern Munich's Franck Ribery.
Meanwhile, a David Villa penalty earned Valencia a deserved 3-2 Group B win at home to Genoa to end a four-game winless streak.
David Villa scored both goals as the pre-tournament favourites bounced back from their shock defeat by Switzerland, but Del Bosque was left unimpressed.
David Villa -- who also came on as a substitute -- rounded off a resounding win for Tito Vilanova's men with a injury-time strike.
"The signing depends on Ibrahimovic, on Eto'o and all parties, " said Barca president Joan Laporta, who is also keen to sign Valencia's David Villa.
European champions Spain survived a stern test from Portugal to book their place in the quarter-finals of the World Cup through David Villa's goal.
Coach Vicente del Bosque withdrew his misfiring strike-force of Fernando Torres and David Villa in the 58th minute, bringing on David Silva and Daniel Guiza.
While Real sorely missed the suspended Cristiano Ronaldo in Pamplona, Messi underlined his value to the Catalans -- who were without injured striker David Villa.
David Villa, Andres Iniesta and Sergio Busquets started on the bench as La Liga leaders Barca beat Real Zaragoza thanks to a Seydou Keita strike.
For every David Villa, there was a disappointment like Dmytro Chygrynsky.
Zigic came on for Spanish international striker David Villa, who limped off with a hamstring strain and looks doubtful for upcoming World Cup qualifiers next week.
Barca could also have snatched a victory, but David Villa missed a golden opportunity to mark his 100th first-team appearance after coming on as a substitute.
Slavia's Hocine Ragued received a second yellow card before Spain striker David Villa hit the woodwork was then sent off for violent conduct in the 85th minute.
Real had targeted Villareal's Spain international Santi Carzola or Valencia's David Villa after missing out on Ronaldo, but both have recently signed new contracts with their clubs.
Among those to be linked with a move to the Premier League champions are Brazilian forward Douglas Costa, French playmaker Franck Ribery, and Spain striker David Villa.
Valencia's David Villa hit the bar and Nicola Zigic appeared to be pulled down in the box, but Atletico prevailed and will face Liverpool in the last four.
Striker David Villa scuffed a shot which deflected off Diego Godin and -- apparently going wide of the goal -- then hit Gabi before bobbling into Thibaut Courtois' net.
Playing without David Villa, their all-time leading scorer who missed the tournament with a broken leg, the Spaniards had found goals hard to come by coming into the final.
Spain had great chances in the second half with David Villa denied by the legs of Heitinga, and Sergio Ramos who headed over with the goal at his mercy.
Forlan polled 23.4 percent of votes cast by journalists covering the World Cup, to finish ahead of Dutch playmaker Wesley Sneijder (21.8 percent) and Spain striker David Villa (16.9%).
David Villa and substitute Cristian Tello scored in the second half before Getafe hit back through striker Alvaro Vazquez, but then Andres Iniesta and defender Gerard Pique netted in time added on.
It was Spain's trademark style, and the team played accordingly, using either a small, dead-eye striker like David Villa or the fleet-footed Fernando Torres up front to deliver the final blow.
Just 10 minutes of the second period had elapsed when Kevin Constant's dreadful error allowed Xavi's pass to skip into the path of David Villa, who curled an exquisite effort into the far corner.
David Villa snatched a late winner to book Spain's first appearance in a World Cup semi-final as they beat Paraguay in a largely disappointing quarter-final tie that nonetheless boasted moments of incredible drama .
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