Samuel Chukwueze was helpless as Sadio Mane scored the winner to help Liverpool see off a spirited challenge from Villarreal.
Chukwueze had started the first leg at Anfield, but he delivered an underwhelming performance. Still, he was expected to feature from the start on Tuesday. However, Villarreal coach Unai Emery decided to pair Boulaye Dia and Gerard Moreno up front.
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Going into the game, Villarreal knew they needed a positive and fast start if they were to upset the odds. And they did just that when Dia put them ahead three minutes into the game.
The Senegalese striker tapped home from inside the box following a low cross from the Etienne Capoue. Dia's goal lifted the home crowd and increased the energy of the Yellow Submarines.
Liverpool had dominated the first leg, but they had no answers to Villarreal's pressing in the opening half. Jurgen Klopp's men struggled to contain the home side and could not string passes together.
Villarreal continued to press for the second goal and almost got it through Giovanni Lo Celso, but the Argentine was stopped by Alisson Becker in Liverpool's goal.
However, their pressure finally paid off five minutes from half-time as Francis Coquelin headed home a cross from Capoue to double their advantage.
His goal meant both sides went into the break with the aggregate scores tied. Knowing they had to play better, Liverpool resumed the second half on the front foot.
There was more urgency in their play as Villarreal sat back to defend their two-goal lead. But the Yellow Submarines could not hold on for too long as Liverpool pulled one back in the 62nd- minute through Fabinho.
The Brazilian midfielder's shot from the edge of the box went through the legs of Geronimo Rulli, who should have done better.
Fabinho's goal put Liverpool ahead on aggregate, and there was only one outcome from that moment. Five minutes later, the Reds drew level through half-time substitute Luis Diaz, who headed home a cross from Mohamed Salah.
Emery reacted by bringing on Chukwueze, but the tie was already over by the time he entered, meaning he had no impact. Liverpool then completed the comeback in the 74th-minute when Mane capitalised on Rulli's mistake to slot into an empty net.
Mane's goal sealed a 5-2 aggregate win for Liverpool, but the Yellow Submarines would be proud of their performance. Jurgen Klopp's men will now meet the winner of Real Madrid vs Manchester City in this season's showpiece at the Stade de France on May 28.