United, which won Europe’s second-tier competition in 2017, will meet Sevilla or Wolverhampton Wanderers on Sunday for a berth in the final after grinding down the Danes and its inspired goalkeeper Karl-Johan Johnsson in an entertaining game.
Sevilla, which has lifted the Europa League trophy a record five times, faces Wolves in Duisburg on Tuesday while 2009 winner Shakhtar Donetsk takes on FC Basel in Gelsenkirchen.
Copenhagen dominated the opening half and missed several chances, with United’s defence looking all at sea in the opening 20 minutes as it made several desperate clearances to deny Mohamed Daramy and Jonas Wind.
United thought it had taken the lead on the stroke of halftime but Mason Greenwood’s precise shot into the far corner was correctly ruled out for offside after a VAR check. Being on the back foot in the opening half spurred United into action though and it created a flurry of chances after the break, although Wind also came close at the other end.
Fernandes settled the contest when he drilled his spot-kick past Johnsson after Anthony Martial, who saw several sitters thwarted by the keeper, was fouled by Andreas Bjelland.
Meanwhile, Inter Milan striker Romelu Lukaku scored the winner in a 2-1 victory over Bayer Leverkusen as he tormented the Germans to lead his side into the semi-finals.
Nicolo Barella put Inter ahead after 15 minutes, driving the ball home after Lukaku’s shot was blocked, and six minutes later the Belgian got on the scoresheet when he displayed his strength by holding off defender Edmond Tapsoba before firing home.
Leverkusen winger Kai Havertz, reported to be a transfer target of Premier League club Chelsea, pulled a goal back for the German side but it was goalkeeper Lukas Hradecky who kept it in the game with a string of fine saves.
After scoring what proved to be the winner, Lukaku could have had a second goal when Inter was awarded a penalty for handball, but that harsh decision against Leverkusen was overturned by the Video Assistant Referee (VAR).
Lukaku showed plenty of humility after his dominant performance, saying: “To me, the man of the match is Nicolo Barella. The way he plays football is simply incredible - maturity, quality. He is truly a great player.” RESULTS: Manchester United 1 (Fernandes 95-pen) bt FC Copenhagen 0; Inter Milan 2 (Barella 15, Lukaku 21) bt Bayer Leverkusen 1 (Havertz 24)