The result in their quarter-final, second leg at a boisterous Sanchez Pizjuan stadium put the Andalusians through 6-3 on aggregate and set up a semi-final against Real Madrid or their city rivals Atletico, who meet on Thursday.
Real, who have not won Spain's domestic Cup since 1993, have a 3-1 advantage from last week's first leg at the Bernabeu.
Brazilian midfielder Renato fired Sevilla ahead in the seventh minute when he belted the ball into the net after Alvaro Negredo had beaten goalkeeper Diego Lopez with a dinked effort that was about to roll over the line.
Villarreal's chances were effectively extinguished when the home side struck twice shortly after half-time.
Both goals came from corners swung over by Ivory Coast midfielder Ndri Romaric, his fellow African Frederic Kanoute of Mali nodding in the first and Alexis Ruano the second three minutes later.
The party atmosphere was a fitting setting for the return to action of Sevilla defender Sergio Sanchez after surgery on a heart condition and an absence of more than a year.
"I felt very well and very comfortable," Sanchez said in a television interview.
"I want to thank my team-mates who have made everything easier for me," he added.
Barcelona, the 2009 winners, are virtually assured of their semi-final spot after they thumped second-division leaders Real Betis 5-0 in the first leg.
Pep Guardiola's side, who set a new club record of 28 matches unbeaten in all competitions on Sunday, play at Betis on Wednesday.
They would meet Almeria or Deportivo La Coruna in the last four, with Almeria holding the advantage after winning the first leg at home 1-0.
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