Romelu Lukaku scored on his competitive United debut but Zinedine Zidane's all-conquering Real Madrid side proved too strong for the Reds in Skopje.
This was Real's sixth trophy in 18 months since the legendary Frenchman took charge, and his awesome outfit continue to throw down the gauntlet for others to try and follow.
The twelve-time European champions dominated for much of the contest and powered into a 2-0 lead through Casemiro and the metronomic Isco.
Lukaku - who had earlier missed a sitter - pulled a goal back and the Reds then almost forced extra-time as substitute Marcus Rashford went close in a late rally.
Despite the defeat, there's much to be positive about as new signing Nemanja Matic enjoyed an impressively eye-catching debut at the heart of United's five-man midfield.
Reported Reds target Gareth Bale fired wide from close range early on and Casemiro struck the crossbar before the Champions League holders went ahead on 24 minutes.
Despite looking marginally offside, the Brazilian midfielder volleyed in beyond David de Gea after he latched on to Dani Carvajal's superbly weighted through ball.
Real continued to press and De Gea saved well from Karim Benzema and Toni Kroos either side of the interval.
The second goal was not long in coming for the Spanish champions, though, as Isco slotted home after neat link-up play with Bale on 52 minutes.
Victor Lindelof, Nemanja Matic and Lukaku all made their competitive United bows, and the latter should have done better with a gilt-edged chance five minutes after the goal.
Keylor Navas parried Paul Pogba's header and the loose ball fell to Lukaku - well placed eight yards out - but he wastefully blazed over the top.
Bale struck the bar but it was game on less inside a minute when, this time, the Belgian made no mistake on the rebound from a saved Matic shot.
The Reds mounted a gutsy late surge with half-time substitute Rashford in particular looking lively.
Having burst clear one-on-one, he came close to taking the tie into extra-time, but Navas saved well and tipped his low effort around the post.
Fellow substitute Marouane Fellaini also went close with a late header, but Real held on to take the spoils in the first ever Super Cup meeting between the heavyweights.
Overall team performance: 6.5/10
United Faithful Man of the Match: Nemanja Matic. An impressive debut