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Two first half goals from Manchester City's David Silva and a David Villa strike were enough for Spain who top the group with a 100 percent record from eight matches.
Scotland's consolation came from a David Goodwillie penalty on 64 minutes after Victor Valdes had tripped Steven Naismith.
Afterwards Spanish coach Vicente Del Boque summed up his side's philosophy and style.
"Up against two big centre-halves we've looked for our small men to score the goals," he said.
Silva, who has been in stunning form for Manchester City this season, said he had the formula for getting a regular start weith the national side.
"I just have to continue playing like that" he told Spanish TV afterwards, "we've passed and played well so we are happy."
Scotland manager Craig Levein was positive about his team, even though they failed to deliver at the end of qualifying Scotland's first appearance at a major finals since the 1998 World Cup finals.
"The result is disappointing, our hope tonight was they came down ten or fifteen per cent, but they were pretty close to the maximum and like that they are difficult to play against," said Levein.
"I have to give our guys enormous credit, on another day we could have had three or four goals," he said.
The home team were determined to show why they are reigning European and World Champions and settled into their passing game straight from kick-off, indeed it was two minutes before a Scottish player touched the ball.
As early as five minutes Spain were ahead. Valencia's Jordi Alba, on his debut, found space on the left wing to centre for Silva who finished crisply first time inside the near post.
And by the 15th minute when the Czechs were two goals up in Lithuania, one a penalty awarded by a Spanish referee, it was clear Scotland were going to get little from their trip to Alicante.
Indeed so complete was Spain's dominance, it wasn't until the 19th minute that they conceded a foul.
On 34 minutes Darren Fletcher came close for Scotland with a left footed shot and when four minutes later James Morrison shot high from a wide left position Scottish hopes were momentarily revived.
The Spanish however continued to create and Allan McGregor in Scotland's goal had to make a great outstretched save on 41 minutes from Santi Cazorla.
Three minutes later he could do nothing when Silva cut in from the right wing, exchanged passes with Pedro Rodriguez, and shot into the left hand corner to send the Scots in needing a second half miracle.
On 53 minutes Cazorla, Silva and Xavi Hernandez linked up delightfully on the right to find Villa in space in the Scottish area and the Barcelona striker easily slotted away his 50th goal in international football.
Scotland continued to toil and created more in the second half with substitute Goodwillie in particular providing some much needed spark in attack.