The Red Devils made the perfect start to the match, with Fernandes dispatching an unstoppable penalty in the top corner after Marcus Rashford had been brought down by Diego Carlos.
Sevilla responded through Suso midway through the first half, though United dominated the match after the restart and created a host of chances only to be denied by goalkeeper Bono.
Then, in the 78th minute, United – and Lindelof in particular – switched off at the back as a cross into the box found an unmarked Luuk de Jong who tapped in from close range to knock Ole Gunnar Solskjaer’s side out.
Fernandes was clearly fuming and confronted the Swedish defender before kicking off again, bemoaning his mistake, though Lindelof was in no mood to take responsibility as the teammates yelled and swore at each other.
After the defeat, Fernandes fronted up to the media and addressed the row with Lindelof, saying it is a ‘normal’ part of football and they will put it behind them quickly.
Asked about the confrontation, the January signing from Sporting told BT Sport: ‘I think it’s normal, you know, when you [concede] a goal in the last [minutes]. We have 10 minutes after to score again.
‘Everyone was mad, you know. It’s not about me or Victor, it’s about every team.
‘What happened between me and Victor is nothing. It’s normal, it’s football, it happens. It’s looking for each other, you know.
‘There will be much more times these things happen in other teams and everything. The most important thing now is we need to see the mistakes everyone did and look forward to improve in the next games.’
United’s defeat ends both their Europa League campaign and a season that started a year ago, with Solskjaer’s side making plenty of progress but ultimately losing in three semi-finals across Europe and the domestic Cups.