After a week of protests and the reveal of a shiny new stadium, United were desperate for a tonic on the pitch, and head coach Ruben Amorim knew the value of progressing in a competition that represents their only chance of glory in a flailing campaign.
The fallen giants made a torrid start, however, when Matthijs de Ligt brought down Mikel Oyarzabal in the penalty area, with the Spaniard duly dispatching his subsequent spot-kick, just as he did in the first leg.
Any United comeback was always likely to come via the talismanic Fernandes.
After scoring a stunning free-kick against Arsenal on Sunday, the Portuguese midfielder displayed his dead ball capabilities again when caressing his penalty into the net after Igor Zubeldia had impeded Rasmus Hojlund in a similar manner to De Ligt’s foul prior.
Despite two penalties within the space of six minutes, the pace of the game refused to relent as the Red Devils grew.
But on the half-hour mark their golden chance went begging when Hojlund, who came into this clash on a 20-game scoreless streak, skewed his close-range effort wide of the post.
Barely two second-half minutes had passed before the official pointed to the spot once more after Aritz Elustondo had upended Patrick Dorgu.
An ultra-confident Fernandes subsequently sent the keeper the wrong way again for a fifth goal from his last six United appearances.
The second blow clearly dented La Real’s spirits as the hosts began to stroke the ball around the pitch with the confidence expected from a side who had suffered just one home defeat from 29 Europa League matches heading into this contest.
It was Dorgu’s speed which was the spark for more drama again just after the hour mark. Jon Aramburu was sent off for pulling the marauding wing-back down as he marched through on goal, even if the Dane was only 10 yards clear of the halfway line when he was felled.
That was a fatal blow to a Sociedad side currently sitting in the bottom half of the LaLiga standings, and Fernandes sealed his hat-trick in style late on after smashing an effort across Alex Remiro and into the bottom corner.
Diogo Dalot added a fourth in stoppage time by rifling home from Hojlund's cutback to ensure United sailed into the next stage of the competition, where they will meet Lyon.
Flashscore Man of the Match: Bruno Fernandes (Manchester United)