The Welshman took advantage of an error from Chechu Dorado to chip home the opener before setting up Karim Benzema to put Madrid on the road to victory yesterday.
A wonder strike from Villarreal right-back Mario Gaspar gave Villarreal hope before half-time, but the in-form Jese Rodriguez made it 3-1 just after the hour mark with a lovely deft finish.
Giovani Dos Santos' free-kick halved the deficit once more before Benzema's second of the game sealed the points 15 minutes from time.
Atletico were dealt an early blow as goalkeeper Thibaut Courtois missed out due to injury and the Belgian's absence was to prove vital as his deputy Daniel Aranzubia endured a nightmare evening.
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After a keenly contested first-half short on clear-cut chances, Atletico had started the second period strong as Diego Ribas flashed a shot just wide.
However, disaster struck for Diego Simeone's men 10 minutes from time when Aranzubia flapped at Verza's overhit cross and the ball flew into the far corner.
Having made all three substitutions, midfielder Gabi had to go in goal and Verza converted from the spot with ease.
It was a far happier evening for Real at the Santiago Bernabeu and boss Carlo Ancelotti hailed Bale's contribution in Ronaldo's absence.