The German football team won all of the 13 matches they competed in, claiming their first European title since 1980.
Eintracht Frankfurt fans left Barcelona stunned at Camp Nou on Thursday as they took over the stadium, sparking a policy change in the club over the sale of future tickets.
Frankfurt go through to the last four and the German club will now be eyeing a first European triumph since they won the UEFA Cup in 1980.
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.
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