Villarreal produced a spirited second-half performance despite being reduced to 10 men, but were undone on the break late on.
Getafe were gifted the lead in the fifth minute when Ciprian Marica capitalised on some poor defending, robbing the goalkeeper of the ball and slotting into an empty net.
Giovani dos Santos then placed a delicate chip wide before seeing an effort cleared off the line as Villarreal started to dominate the game.
Their resurgence was dampened just before half time though, when Pablo Iniguez was shown a red card after brining down Marica, who was clean through on goal.
After the break there were few clear chances despite the visitors' man advantage.
Getafe did manage to make the game safe in the last minute as Pablo Sarabia produced a neat finish after a counter-attack left him in lost of space.