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 re-start.
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.
A disappointing Brazil beat South Africa 1-0 in a friendly but the lacklustre performance cast further doubts on Mano Menezes's long-term prospects as Brazil coach.
Menezes sent out an attacking team but they struggled to break down the dogged South Africans and the match was only decided in the 74th minute with a goal from second-half substitute Hulk.
The striker signed by Zenit St Petersburg last week for 55 million euros had been on the pitch for less than 10 minutes when he pounced on a rebound to turn and smash the ball home from 12 yards.
Menezes acknowledged the team did not gel but said fans' boos that began in the middle of the first half were not helpful.
"(The boos) are uncomfortable," he said. "The younger a team is the more it feels the lack of support."
Menezes took over in July 2010 and dispensed with the old guard in favor of youngsters like Neymar, Lucas, Thiago Silva and Oscar.
Although his team have won 22 of their 33 matches, they have failed to overcome top-class sides like Germany, Argentina and the Netherlands.
The former Corinthians coach is under pressure to produce an exciting and winning side ahead of the 2013 Confederations Cup and 2014 World Cup, both of which will be held in Brazil.
His players struggled to impose itself against a team 62 places below then in the world rankings and it was not until he introduced Hulk and several others that Brazil began to create real chances.
"We lost a little bit of control of the game for 15 minutes in the second half, but with the substitutions we took control again and that was enough to give us a result," Menezes said.
"I don't think we played really badly. Maybe we didn't play well but we weren't really bad."
Brazil's next match is against China in Recife on Monday.