The Yellow Submarine made the trip to the capital on the back of an away win over Valladolid in the first week of La Liga fixtures.
They also picked up a European win during the week, and they continued their fine form with a disciplined away performance at the Civitas Metropolitano.
There were chances for both sides to take the lead, though Matheus Cunha had the best of them just after the midway point in the second half, with Geronimo Rulli doing enough to put him off.
And moments later, Villarreal were in front when Yeremy Pino pounced on a Molina mistake with a sweet finish into the far bottom corner.
Yannick Carrasco - and indeed the whole stadium - thought he had scored an equaliser shortly after, but Rulli somehow managed to pull off a magnificent save to prevent the ball from crossing the line by a couple of inches at best.
Having survived that almighty scare, Villarreal were confident in seeing out the win, and things got even easier when Molina shoved Alex Baena off the ball, getting a red card for his troubles.
Gerard Moreno then got off the mark in his La Liga season slotting one home late in stoppage time to wrap up the three points, with Unai Emery defeating Diego Simeone for the first time.
Moreno was booked for doing his usual celebration, strangely, with the referee feeling he provoked fans and opposing players. Answers on a postcard.
But the three points is the most important thing, and this was a huge win for the Yellow Submarine as they look to mount a top four challenge this season.
A trip to Croatia to take on Hajduk Split awaits on Thursday, ahead of a return to the capital to face Getafe in the third of three straight away games to kick off the La Liga season.