Barcelona striker Villa, back in the national team for the first time since breaking his leg at the Club World Cup in December, came on as a substitute and netted his side's fourth goal from the penalty spot in the 63rd minute.
Spain's all-time leading scorer took his tally to 52, while his club team-mate Pedro weighed in with a double, and Santi Cazorla and Xavi also got on the scoresheet against Frank Rijkaard's visitors.
"I'm pleased to be back here again." Villa told Spanish television. "I have really missed all this. Not only the games but also being with the team. I can put everything behind now me and start to look forward to enjoying myself again."
Chelsea forward Torres, who scored the winner for Spain in the Euro 2008 final, started out as captain and became the youngest of six Spaniards to have reached the 100 mark, aged 28.
New Arsenal signing Cazorla struck first for the hosts when he pounced on a parried shot in the 23rd minute, and Pedro doubled the lead with a neat lob.
Xavi came on as a half-time substitute and his first touch of the ball was to curl a free-kick into the top corner straight after the restart.
Villa received a huge ovation when he replaced Torres in the 53rd minute and, just as he did on his official return for Barcelona last month, scored within minutes of entering the field of play.
Ignacio Monreal was brought down for a penalty and Villa sent the keeper the wrong way before Pedro sealed the victory with another deft finish after bursting away from the Saudi defence.
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