This is the Spanish club's first major title in their history. Villarreal defeated United 11-10 in penalties to lift the Europa League title.
But it will not be Premier League rivals Arsenal they meet in Poland's Gdansk on May 26, rather Spaniards Villarreal, who are in a first major final after a goalless second leg in London, DPA reports.
Fernandes opened the scoring for United in the ninth minute but Lorenzo Pellegrino levelled with a penalty and Edin Dzeko put Roma ahead in the 34th, DPA reported.
Marcus Rashford's fine goal and a late Bruno Fernandes penalty in Spain last week put the Red Devils in control of the quarter-final tie heading into Thursday's reverse fixture at an empty Old Trafford.
With the tie finely-poised following a 1-1 home draw a week ago, the Gunners put in one of their best showings under Mikel Arteta to win 4-0 in Prague, DPA reported.
United won the first leg of the Europa League quarter-final by 2-0 against Granada. Rashford opened the scoring for visitors as he netted the ball in the 31st minute of the match before the late penalty strike
Midfielder Pogba, on his return from injury, fired in high at the near post in the 49th minute on Thursday to give United the honours in the battle between former European champions, DPA reported.
AC Milan defender Simon Kjær capitalised on poor defending to head in a corner in the 92nd minute to give the Italian side a slight advantage ahead of the second leg next week
Aubameyang scored twice for Arsenal, including the decisive 87th-minute winner just as the Gunners were poised to go out on the away goals rule despite playing both games abroad
The teenage forward replaced Mason Greenwood in the 76th minute of United's 0-0 draw with Real Sociedad at Old Trafford. As a result, he became the club's youngest ever player in a European match, at the age of 17 years and 23 days.
Yazici, who is yet to start in Ligue 1 this season, stole the show with his hat-trick at the San Siro
Tottenham saw their 10-match unbeaten run end, despite having Gareth Bale in the starting lineup for a second straight time in the competition
North London rival Arsenal on Thursday opened their fourth straight Europa League campaign with a 2-1 come-from-behind win at Rapid Vienna in an opening round of games affected by the coronavirus pandemic.
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