Pedro, Santi Cazorla and Xavi had already put the world champions in a commanding position by the time Vicente del Bosque introduced Villa for Fernando Torres, and Spain's all-time leading scorer soon had his 52nd international goal as he stroked home a penalty 27 minutes from time.
And it was Pedro who completed the rout 10 minutes later as he raced onto David Silva's pass to chip in his second goal of the evening.
Del Bosque started with only three of the side that began the Euro 2012 final with Nacho Monreal, Juanfran and Benat Etxebarria among those given a chance to impress, as was Torres and he was also handed the captain's armband for his 100th appearance in the absence of Iker Casillas.
A Torres goal was all that was missing from an extremely comfortable evening for Del Bosque's men against a Saudi side that looked out of their depth from the beginning.
Torres was first to threaten as he sped onto a neat pass in behind the Saudi defence, but a poor first touch from the Chelsea forward saw the ball run through to Waleed Abdullah.
Cazorla and Pedro though were looking the more likely to make the breakthrough and it was no surprise when the two combined for the opening goal on 23 minutes. Pedro cut inside two soft challenges on the left and, when his fierce right-footed effort was beaten away by Abdullah, Cazorla was on hand to sweep home his fourth goal in his last six appearances for Spain.
Benat then came within inches of his first international goal as his shot came back off the post after being fed by the busy Pedro, but the world and European champions were nearly stunned seconds later when Naser Al-Shahrani flicked a header inches wide of Victor Valdes' right post.
Normal service was resumed, though, when Pedro timed his run perfectly to meet a Cazorla through-ball and finished beautifully with a lob over the helpless Abdullah.
Cazorla then hit the bar and Torres fired just over with his last chance of the evening as the hosts threatened to run riot before the break. However, Del Bosque refused to take it easy on the visitors after the interval as Sergio Ramos and Xavi replaced Gerard Pique and Cesc Fabregas, and it was Xavi who made it three with virtually his first touch as he curled a brilliant free-kick into the top corner on 47 minutes.
Villa was next to be introduced, making his much-anticipated return to international football, and he was given the perfect opportunity to mark it with a goal when Monreal was brought down inside the area by Sultan Al-Bishi.
The Barcelona striker sent Abdullah the wrong way from 12 yards and the Saudi keeper was beaten again before the end as Pedro rounded off his fine display with another dinked finish from Silva's through-ball.