Gareth Barry crossed from the left for Villa team-mate Agbonlahor but the striker volleyed narrowly wide.
Barry then headed a Stewart Downing corner wide before Emile Heskey was cynically fouled when he would have been clean through on goal, although he was wrongly given offside.
But the early England promise quickly evaporated as Spain found their passing rhythm and, at times, toyed with the visitors.
Everton's Jagielka was making his first England start and facing Fernando Torres of Liverpool for a fourth time in the past four weeks.
The centre-back had come out on top in their previous duels and, when Torres created a sight of goal for himself, it was Jagielka who flung himself to block the striker's shot and also clear after a David James fumble.
But Spain could also call on Euro 2008 Golden Boot winner Villa, who profited from Jagielka's error that led to Spain's opener.
Beckham honoured to match Moore's record
His stray pass found Xabi Alonso, who swiftly fed Villa. He skipped past Jagielka and held off John Terry's challenge before expertly side-footing home into the bottom left-hand corner.
The sight and danger of Spain's front two highlighted England's lack of a proven goalscorer, despite Heskey's nuisance factor and Agbonlahor's pace.
Spain were in their stride and, after a Villa shot was blocked by Terry, Alonso struck a powerful shot off target.
There was a regality about the Spanish midfield, with Xavi and Andres Iniesta stroking the ball around with ease.
Barry and Michael Carrick were in the centre of England's midfield to nullify Spain but the pair had little impact and spent most of the game chasing their rivals.
The raft of substitutions at half-time included the arrival of Beckham, who drew level with 1966 World Cup-winning captain Bobby Moore on 108 caps, the record for an England outfield player.
Beckham's precise cross-field pass found Shaun Wright-Phillips, who cut inside from the left to create a chance for himself only to see his shot saved at the second attempt by Pepe Reina.
England's defeat was sealed eight minutes from time when Llorente rose above Matthew Upson to power home a header from Xavi's diagonal free-kick.
Cole had a chance to reduce the arrears late on from Beckham's superb through-ball when the West Ham striker, on for his England debut, went round Reina but saw his shot cleared off the line by Gerard Pique.
In a fractious final few minutes out of keeping with the rest of the match, Beckham was booked for dissent.
Defeat, the second of his reign, by the world's number-one ranked team left Capello with plenty to reflect on ahead of next month's friendly with Slovakia, before the key World Cup qualifier against Ukraine.
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