The 29-year-old Asturian striker's 45th and 46th goals for his country on his 72nd appearance made him the nation's leading scorer in his own right, two clear of Raul, who won his 102nd and last cap for Spain in 2006.
Nicknamed "el guaje", or "the kid", Villa's five goals in South Africa last year helped the Iberian nation to their first World Cup triumph and he was the leading marksman at Euro 2008 when Spain won their second continental championship.
"I really wanted it [the record], especially because it was a very tough match that did not start as we had hoped," Villa told reporters.
"I promised Pepe, who is my friend, a while ago that the goal that exceeded Raul's tally would be for him and I went over to dedicate it to him."
Spain's 10th victory in a row in competitive games since they lost to Switzerland in their opening match at last year's World Cup puts them in firm control of the group ahead of Tuesday's trip to Lithuania.
Friday's match was the 100th cap for Spain playmaker Xavi, Villa's Barcelona team mate whose domination of possession and distribution of the ball in midfield has been a crucial element of the recent successes of his club and country.
"I am happy, pleased to have got to 100 games, but also filled with a desire to continue participating and playing in this team, in which I have a magnificent role right now," the 31-year-old said.
