Pervis Estupinan scored an own goal, coupled with a Sadio Mane strike in the second half to earn an advantage for Liverpool heading into the second leg of the Champions League semi-final next Tuesday.
The win on Wednesday keeps their quadruple bid alive.
Estupinan deflected team captain Jordan Henderson’s cross into his own net in the 53rd minute and Sadio Mane got the second two minutes later.
The result left the six-time winners well-placed for the return leg in Spain on Tuesday.
Villarreal, who had stunned Juventus and Bayern Munich in the previous rounds, had frustrated Liverpool in the first half before being well beaten.
They created no serious scoring opportunity with just one attempt, compared to Liverpool’s 20.
Jürgen Klopp’s Reds have already won the League Cup, are in the FA Cup final against Chelsea and trail Manchester City by one point in a fierce Premier League title duel.
Should they reach the Champions League final on May 28 in Paris, Pep Guardiola’s Manchester City could also be their opponents there.
This was after Manchester City beat Real Madrid 4-3 in a thrilling other first-leg semi-final on Tuesday.
“They are a very organised team and we knew they would make it difficult.
“It was just important that we kept going and believed that we would eventually break them down. We did that with two good goals,” Henderson said.
But he warned that “the game is still alive and it will be tough in Villarreal.”
Villarreal defender Pau Torres shared this view, insisting that “there’s a lot of football left in this semi-final yet.
“We go home beaten by two goals but we stay confident. Should we score in the first 10 minutes next week we are back in the tie,” he said.
Mane had two early chances as Liverpool made their presence felt.
The first was when he was not able to properly control a ball headed on by Ibrahima Konate.
He then did not manage to head on target when completely unmarked off Mohamed Salah’s cross from the right.
Villarreal sat deep giving the hosts little space as Liverpool mainly tried their luck from a distance.
Thiago Alcantara came closest in the 42nd minute when his long-range drive crashed against Villarreal’s right post.
Fabinho had a goal five minutes after the restart disallowed because Virgil van Dijk was offside before heading on the ball.
Liverpool were finally awarded for their efforts three minutes later.
That was when Henderson’s cross bounced of Estupinan’s foot and high over goalkeeper Geronimo Rulli into the far left corner.
And Anfield rejoiced again 120 seconds later when Salah picked out Mane who beat Rulli for 2-0 with a low shot.
Villarreal were now in danger of falling apart against the relentless Reds.
Andy Robertson was offside before volleying home and Luis Diaz aimed inches right.
The visitors settled down again in the later stages but created no danger up front and face an uphill battle to reverse matters at home next week.(dpa/NAN)