Gerard Moreno gave Villarreal the lead 29 minutes into the Spanish club's first European final, but Edinson Cavani equalised early in the second half before Unai Emery's team prevailed on spot-kicks, extending United's four-year trophy drought.
The winner of the Uefa Europa League earns an automatic spot in the far more lucrative Uefa Champions League.
Arsenal beat Irish team Dundalk, which prepared for their biggest game in recent memory, making Arsenal top of Group B on six points and Dundalk at bottom with no points.
AC Milan withstood a late onslaught to beat Celtic 3-1 and AZ Alkmaar overcame the loss of 13 players with positive Covid-19 tests to secure a shock 1-0 win at Napoli.
Clubs are still in crisis management mode and the full picture would not be known until annual accounts begin to be published within weeks, the president of Italian champion Juventus said.
Sevilla clinched the Europa League title with a 3-2 win over Inter Milan after an overhead kick by defender Diego Carlos deflected by the Italian side's top scorer Romelu Lukaku settled a thrilling contest.
The President of the French Football Federation also added that all football league seasons are over, raising questions over which teams will head to the Champions League.
No sport has been played in Italy since March 9 as the country grapples with the Covid-19 crisis which has killed over 25,000 people.
Uruguayan forward also charged by police in Scotland after the incident in the Europa League on February 27.
The decision was taken after Arsenal manager Mikel Arteta and Chelsea winger Callum Hudson-Odoi tested positive for coronavirus, while Everton announced their entire team had gone into self-isolation after a player reported symptoms of Covid-19.
Arsenal Head coach Mikel Arteta has tested positive for the coronavirus, forcing the club to close its training complex and put the entire first-team in self-isolation.
The five-time Ballon d'Or winner is closing in on the all-time Serie A record of scoring in 11 consecutive games held by Gabriel Batistuta and Fabio Quagliarella.
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