The match against the European Champions in Seville was a chance for England coach Fabio Capello to assess how far his side has advanced and the midfield did a good job of closing down Xavi and Andres Iniesta in the opening half hour.
However, a careless pass by defender Phil Jagielka let Spain in to score the opener on 36 minutes.
Xabi Alonso picked up the loose ball and fired it to Villa who jinked his way past several England defenders and sent a low shot past David James, the sixth match in a row the Valencia striker has been on target for his country.
Beckham equalled the record of 1966 World Cup winning captain Moore when he came on at halftime at the Sanchez Pizjuan, one of five changes made by Fabio Capello at the break.
The home side continued to dominate a toothless England and substitute Llorente doubled their lead when he outjumped the English defenders to nod past Robert Green with just under 10 minutes remaining.
Spain, ranked number one in the world by FIFA, are now unbeaten in 29 matches stretching back to a 1-0 defeat against Romania in Cadiz in November 2006 and Capello was full of praise for their performance.
"This is a team that knows how to play the ball around and at the right moment, when you make a mistake, they kill you," the former Real Madrid coach said at a news conference.
"They still have the same players and are playing in the same style as when they won the European Championships and they are obviously feeling in great shape on the pitch."
England were without several regulars, including injured midfielders Steven Gerrard and Joe Cole and Manchester United striker Wayne Rooney and they hardly threatened the Spain goal.
A long-range effort from Shaun Wright-Phillips and a Carlton Cole shot cleared off the line were the only real chances in the second period.
Gabriel Agbonlahor had a decent opening early in the first half but sent his volley just wide while Emile Heskey laboured up front to little effect before being replaced at the break by Peter Crouch.
Spain coach Vicente del Bosque said he was happy with the team's long unbeaten run but his priority was the World Cup qualifier against Turkey on March 28 in Madrid.
Spain and England both top their qualifying groups for the tournament in South Africa with four wins out of four and England's next match is against Ukraine at Wembley on April 1.
"For the first few minutes we were a little bit lost but we gradually became better and better," Del Bosque said of his side's showing on Wednesday.
"It's not only the quality of the way we play that's the key but it's also the spirit in the squad."
