Euro 2012 qual. - Silva ends Scotland's play-off hopes
Scotland knew they had to defeat the world and European champions away from home to claim a play-off spot if Group I rivals Czech Republic downed Lithuania in Kaunas.
That unlikely prospect was buried early on in both matches as Silva cracked Jordi Alba's run and pass under visiting goalkeeper Allan McGregor on six minutes to give Spain the lead.
A penalty from Michal Kadlec on two minutes and two more goals from Jan Rezek (16, 45) enabled Czech Republic to open up a 3-0 lead over a poor Lithuania team at half-time on their way to a one-sided 4-1 victory.
Darvydas Sernas and Kadlec shared penalties in the second period, but the visiting side's play-off place was already in the bag.
Scotland's prospects became bleaker when Silva tucked away his second goal of the game on 44 minutes when he worked a lovely one-two with Pedro before slamming a shot through the legs of Christophe Berra from 18 yards to give his side a 2-0 advantage as McGregor failed to claw it out.
Spain moved 3-0 clear on 54 minutes courtesy of David Villa's 50th goal in 80 appearances for his country before Scotland rallied in the final 35 minutes as substitute David Goodwillie tucked away a penalty on 65 minutes after Victor Valdes had fouled the tireless Craig Mackail-Smith.
Scotland's long absence from a major tournament finals will continue at least until the World Cup finals in Brazil 2014. They last qualified for such a competition at the World Cup finals of 1998 in France.
Spain ran out group winners with a perfect record of 24 points from eight games with the Czechs collecting 13 points in second spot from their eight outings. Scotland finished third on 11 points.
Spain's 3-1 victory was probably a true reflection of the evening as Vicente del Bosque's produced their usual brand of immaculate passing play without ever needing to find an extra gear.
McGregor made two excellent saves to keep out shots from Santi Cazorla in the first half, but Scotland also had their moments despite being forced to live off scraps on the break.
Barry Bannan threw over a lovely cross on nine minutes with Naismith just failing to direct the ball goalwards at the back post while Darren Fletcher lifted an effort over the bar from Naismith's headed flick on 32 minutes.
Silva almost netted his hat-trick on 48 minutes after Naismith had squandered possession, but his shot flew narrowly wide.
He made no mistake in punishing the Scots on 53 minutes as he cut open the defence before rolling the ball into the path of Villa to finish with some style with McGregor given no chance.
With Carles Puyol, Xavi and Silva departing the action for Spain with 25 minutes left, Scotland began to find more space in the Spanish defence. Incredibly, they could easily have been level within moments of Goodwillie scoring, but were undone by a lack of finesse.
Goodwillie should have played in Mackail-Smith for an easy tap-in rather than bundling a shot over the bar on 70 minutes before Mackail-Smith hesitated when he was in behind the makeshift home defence, enabling a red shirt to frantically clear the danger.
Spain were also guilty of squandering late chances as Scotland began to tire.
McGregor stood tall to save from Spain substitute Fernando Llorente on 82 minutes while Cazorla chipped over the bar three minutes from time, but it was all largely immaterial by that stage.