La Roja's slick passing and more clinical finishing were ultimately the difference between the sides in the friendly in Alicante and the European champions stretched their winning run to seven matches thanks to a superb Mario Gaspar volley and a goal from substitute Santi Cazorla.
England were depleted by injury and manager Roy Hodgson started with captain Wayne Rooney on the bench but they were still outplayed all too easily and their 15-match unbeaten run came to a disappointing end.
Spain captain Iker Casillas, who became the first goalkeeper to keep 100 clean sheets in internationals in his 165th appearance, said the signs were positive ahead of the continental tournament in France next year.
Casillas was one of those singled out for criticism after the reigning champions failed to get past the group stage at the 2014 World Cup finals in Brazil.
"Two good national teams with good players met and in the end, in the second half, we managed to get the goals and win the match," Casillas told reporters.
"That is very positive for us heading into the European Championship," added the 34-year-old Porto keeper.
One frustrating aspect of Spain's performance for coach Vicente del Bosque was that Diego Costa again failed to score before being replaced by Juan Mata after just over an hour.
The Brazil-born Chelsea forward, who has netted only once - the third goal in a 4-0 win over minnows Luxembourg - in his 10 outings for Spain, said he feels he is improving.
"It doesn't matter that I didn't score the important thing is that Spain performed well," Costa, who has come under criticism from Del Bosque over his Premier League disciplinary problems, told reporters.
"I am feeling better all the time and participating more in the game," added the 27-year-old.
Asked about Del Bosque's criticism, he joked: "It's normal because sometimes my father and mother don't like what I do."
Spain play another friendly on Tuesday against top-ranked Belgium in Brussels.
(This version of the story was corrected to clarify England run unbeaten not winning in third paragraph)
(Writing by Iain Rogers, editing by Patrick Johnston)
