Beckham's introduction as a second-half substitute allowed him to equal Bobby Moore's record of 108 caps for an outfield player.
But if the midfield maestro is to emulate Moore's World Cup win in South Africa next year, England now know they have plenty of work still to do as David Villa and Fernando Llorente condemned Fabio Capello to his second defeat in 11 games as Steve McClaren's successor.
The evening was not without its encouraging aspects as Emile Heskey and Glen Johnson were among those who shone and Carlton Cole produced a late cameo.
But with Xavi a class above anyone else on the pitch, Spain were simply too good and too effective in too many areas for the visitors.
Thankfully there was no hint of racist abuse from a capacity crowd, which meant they could fully concentrate on the action.
England started brightly too. Had it been a competitive international they really would have had cause to grumble when Heskey was sent tumbling by former Manchester United man Gerard Pique on the edge of the area.
Heskey thought it was a penalty. At the very least it was a free-kick and a red card given the striker had rolled Pique perfectly to give himself a clear sight of goal.
Instead, incorrectly, the offside flag went against him.
It marked the start of an industrious display from the newly installed Aston Villa man.
Partnered by club colleague Gabriel Agbonlahor, Heskey was a constant menace to the Spanish defence, which was missing the formidable presence of Carles Puyol.
Heskey sent one header wide, as John Terry had done earlier, while wide pair Stewart Downing and Shaun Wright-Phillips both caused the hosts problems in their own unique way.
For long periods, it was an absorbing contest between two pretty decent teams, a label that certainly could not have been attached to England 12 months ago as they took their first tentative steps under Capello, trying to make up for the shattering disappointment of what had gone before.
Indeed, as Capello felt it was the defeat to France in his second game that he felt England were a project with promise, he presumably was not too disheartened at eventually falling behind to the European Champions.
It has to be said, some of Spain's passing is fantastic and in Barcelona's Xavi they have one of the most stylish players on the planet right now.
Fernando Torres and Marcos Senna both went close on a couple of occasions and Xabi Alonso threatened the England goal with a rising shot.
As Terry and Johnson were throwing themselves wholeheartedly - and literally at times - at their opponents, England's 4,000-strong travelling army had every reason to cheer.
How galling therefore that Spain's opener should have arisen from a pretty basic error from Phil Jagielka, making his first England start after Rio Ferdinand had pulled out with a stomach upset.
It is difficult to assess precisely what Jagielka was trying to do when he rolled the ball purposefully away from his own penalty area.
The intention was presumably not to give it straight to Alonso in space. He quickly transferred possession to Villa, who only made things worse for Jagielka by skipping past his attempt to make amends, holding off Terry, then sliding a precise shot past David James.
Five changes at half-time included Beckham's introduction for Downing, allowing a player whose career is littered with notable milestones to claim one of the most cherished.
It was Xavi who put his stamp on the second half first though with a magnificent nutmeg of Terry which goaded the England skipper into bundling him over, completely and utterly outfoxed.
Torres departed the scene after 63 minutes, which should meet with Rafael Benitez's approval given the Merseyside title chasers are not in action again until February 23 when they entertain Manchester City.
The introduction of Cole for a 15 minute debut was more notable, or at least it would have been had his first touch been directed goalwards instead of blazing Johnson's right-wing cross over.
There should be no surprise Xavi should provide the free-kick that allowed Llorente to wrap up Spain's victory eight minutes from the end.
Cole still had time to threaten the home goal with a powerful surge that took him past Jose Reina, only for Pique to block the shot that followed, and a bad tempered ending, out of synch with the rest of the contest, saw Beckham booked.
But Capello has plenty to reflect upon ahead of another friendly with Slovakia on March 28, followed by the key World Cup qualifier against the Ukraine at Wembley four days later.