The 2-1 win by Vincenzo Montella's side, who are in fifth place in La Liga and struggling to qualify for next year's competition, cuts United's European campaign short but they only had themselves to blame.
Sevilla have been a shadow of the team that won three successive Europa League titles between 2013 and 2016, with the Spanish side now sitting fifth in the La Liga table, a massive 11 points adrift of the top-four.
In the last five games, Manchester United has won four games and drawn one game whereas Sevilla FC has won two games, lost two games and drawn one game. The intention and the way we started was really good and really positive, then after 10 or 15 minutes of success without goals, Sevilla have a good team they have players who can hide the ball.
The two sides drew 0-0 in the first leg at the Ramon Sanchez Pizjuan Stadium in a game which saw David De Gea make a string of great saves. Earlier this week Michael Carrickconfirmed his retirement from football at the end of the season, and United will be looking to give the midfield veteran a fitting send-off by potentially winning the competition for the second time in Carrick's career.
Clutching desperately at the thinnest of straws, Mourinho suggested United had no time for self-recrimination because they had an FA Cup quarter-final tie against Brighton coming up at the weekend. "I am not frustrated about the first leg".
With United reeling, Ben Yedder soon added his eighth goal of this season's Champions League, De Gea unable to claw out the striker's looping header.
Unsurprisingly Mourinho did not share the critics' view that United had been poor.
Manchester United became the second English Premier League club to be knocked out in the Round of 16 after Tottenham.
"It's a very special game tomorrow night for Seville".
"Even if Paul Pogba was fit I don't think he would get in the United team, as he has suffered from the confusion that Alexis Sanchez's arrival has brought to the team".