In the first European final to be played in front of a crowd in two years amid the COVID-19 pandemic, Villarreal survived a tough second half to give coach Unai Emery a record fourth title in the competition on Wednesday, leaving United without a trophy since their Europa League triumph in 2017.
Gerard Moreno stretched to reach Dani Parejo’s free kick and steered the ball past De Gea to open the scoring in the 29th minute, only for United to level when Edinson Cavani poked the ball home after collecting Marcus Rashford’s deflected shot on 55 minutes.
After no goals were scored in extra time, all outfield players scored their penalties and Rulli coolly beat De Gea before saving the United keeper’s spot kick.
Villarreal were playing their first big final and coach Emery recognised United were favourites due to their more storied history but urged his side to “keep breaking down barriers” after four semi-final exits.
Emery is renowned for his diligent study of opponents and although United made the stronger start, his side managed to minimise their strengths, ensuring Bruno Fernandes was deprived of space to create danger and Cavani had little wiggle room.
Their only chances in the first half were wayward shots from Scott McTominay and Luke Shaw and while Villarreal did not exactly sparkle, they made their one chance count from a free kick given away by Cavani.
Raul Albiol blocked Eric Bailly and Moreno out-muscled Lindelof to slide in and meet Dani Parejo’s curling cross, powering his shot beyond De Gea.
It was Moreno’s 30th goal of the season and saw him become Villarreal’s joint-top scorer of all-time alongside Giuseppe Rossi.
United continued to take the initiative after the interval and levelled with a scrappy goal as Rashford volleyed against a crowd of bodies following a corner and the ball deflected into the path of Cavani, who stroked it into an unguarded net.
The Uruguayan had a couple more half-chances to find the winner while Rashford missed a gilt-edged opportunity but was offside anyway.
Villarreal had barely a sniff down the other end until defender Pau Torres had a chance to find a late winner but failed to keep his shot under the bar.
Villarreal were the better side in the first half of extra time after Emery made all five changes before full time, contrasting with United coach Ole Gunnar Solskjaer, who did not make his first change until the 100th minute.
The five substitutes he did make all scored their penalties in an enthralling shoot-out but De Gea could not keep his nerve and lost the battle with his opposite number Rulli.