10-man Lazio picked up a second Europa League Group G win and heaped further misery on hapless Villarreal and their under-pressure coach Ernesto Valverde.
Substitute Tommaso Rocchi scored an injury-time winner for the Italian side.
Villarreal were the better team before the break but went into the interval on level terms only after Sebastian Eguren had cancelled out Mauro Zarate's effort for Lazio.
Lazio dominated the second period, and even the controversial dismissal of Francelino Ma! tuzalem for a supposed dive in the 68th minute failed to stop Davide Ballardini`s men - who continued to create chances until Rocchi slid home Aleksandar Kolarov's low cross in the 92nd minute.
The Italians move on to six points, three behind leaders Salzburg and three above Villarreal.
Villarreal slumped to the bottom of the Primera Division last weekend but began brightly.
Nilmar should have put them ahead after six minutes when he broke clear but shot wide, with only Albano Bizzarri to beat.
Bizzarri was called into action to tip over Eguren's 25-yard drive before saving another long-range effort, this time from Marcos Senna.
It was all Villarreal early on, but they still found themselves trailing after 20 minutes as Lazio netted with their first serious attack of the match.
A quick ball forward picked out Julio Cruz, who turned inside his marker before feeding Zarate on the far side of the box - and he dinked the ball past Diego! Lopez.
Villarreal did not lose heart, and Ruben Cani s! aw a low drive tipped behind by Bizzarri in the 25th minute - before the away team deservedly equalised just before the break.
Joan Capdevila sent over a brilliant cross from the left, and Eguren charged in to send an unstoppable header just inside the post from six yards out.
Lazio dominated the second half, and Kolarov headed a great chance wide before the impressive Zarate struck the post after racing from inside his own half.
Zarate then had another effort saved by Lopez, before controversy struck as Lazio lost Matuzalem to a red card.
Matuzalem looked to have a good claim for a penalty after he went crashing after nicking the ball away from Ivan Marcano, but referee Ivan Bebek felt the Brazilian had dived and showed him his second yellow card of the match.
Despite that setback, Lazio continued to take charge of the game - and Cruz only narrowly failed to turn Zarate's cross in at the far post. Rocchi, Kolarov and Zarate all also went close in ! the closing stages.
At the other end, Eguren and Senna had gilt-edged chances for Villarreal - and they paid the penalty for wasting those when Rocchi fired through Lopez's legs late on.
