Goals from Fabinho, Luis Diaz, and Sadio Mane saved the Reds from European humiliation against a side who cancelled out their 2-0 first leg deficit with ease.
A third-minute opener from Boulaye Dia raised eyebrows and nerves, before former Arsenal man Francis Coquelin gave Liverpool their biggest shock in years.
Former Republic of Ireland international and talkSPORT commentator Andy Townsend described Liverpool's display as 'insipid', and the stats agreed.
Losing out on possession and shots, it looked like the meticulous planning of Unai Emery had again foiled a European giant, but there was one eventuality he didn't plan for.
Defensive midfielder Fabinho made a rare and unexpected run into the opposition box, and sent the ball through the legs of a below-par Geronimo Rulli to help the Reds regain a stunning lack of composure.
And five minutes later, with 23 minutes to play, it was suddenly game over, with second-half substitute Luis Diaz again seeing Rulli let his header pass through with ease.
Jurgen Klopp's men were finally back in their comfort zone when Mane rounded Rulli for his 24th Champions League goal, which also saw him equal Frank Lampard for knockout goals in the competition.
Former Tottenham and Watford man Etienne Capoue was the best player on the pitch for Villarreal's opening 45, but left La Ceramica with five to go after seeing red.
Liverpool closed out the second half with ease despite their worst start of any game this season, and will now contest for their seventh European Cup in Paris against either Manchester City or Real Madrid.
Breaking news. More follows.