The Yellow Submarine made the tip to Turin knowing they needed to beat Juventus one way or another to progress having drawn 1-1 in the first leg.
They had to ride their luck early on, too, with Alvaro Morata hitting the bar and with Geronimo Rulli forced into a number of good saves.
Villarreal caused the odd problem on the break but largely held on for dear life in a completely open first half that neither of Unai Emery of Max Allegri looked comfortable with.
The Yellows tightened up in the second half and limited Juventus, looking far more assured at the back.
The game changed when Gerard Moreno made his long-awaited return from injury, coming off the bench in the 74th minute.
Though, it was another substitute in Francis Coquelin who won Villarreal a penalty when Daniele Rugani brought him down in the box. A VAR review saw the spot-kick awarded.
Cometh the moment, cometh the man. Gerard slotted the penalty just past Wojciech Szczesny, and Villarreal never looked back.
Pau Torres put them in dreamland, scoring for his hometown club by turning home a second from a corner.
Torres decided to stay at Villarreal in the summer to represent his hometown in the Champions League despite Tottenham having an offer accepted.
That decision paid off, the centre-back scoring to all-but wrap up a quarter-final spot for his team.
And there was more to come. Villarreal had the ball in the net again only for the referee to call it back for a penalty following a deliberate handball from Matthijs de Ligt.
Arnaut Danjuma took the next spot kick, during stoppage time, and he made no mistake.
A 3-0 away win in Turin for Villarreal against one of Europe’s biggest clubs. A quarter-final spot booked against all the odds. Another masterclass from Unai Emery.
How many times can this club be written off?