Casemiro put the reigning European champions in front on 24 minutes on a steamy summer's night in the Balkans and Isco doubled their lead seven minutes into the second half after a one-two with Gareth Bale.
The gulf in class between Madrid -- for whom Cristiano Ronaldo appeared as a late substitute -- and Europa League winners United that Jose Mourinho had feared was all too evident and it looked like the Spaniards would go on to win by a wider margin.
It was to no avail, with Zinedine Zidane's side winning this trophy for the second year running and the fourth time overall. It is the eighth time in nine years that a Spanish club has won the Super Cup.
"It is all down to hard work. We know there is a lot of talent in this team and there is so much hunger too, they always want more," said Zidane after lifting more silverware.
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- Bale handed start -
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While Ronaldo started on the bench for Madrid having only commenced pre-season training at the weekend, Bale was included in the first XI.
United boss Mourinho caused a stir on Monday when he claimed he would make a bid to take the Welshman to Old Trafford if he were not a starter at the Philip II Arena.
Despite the presence of ?75 million ($97 million) signing Lukaku up front, with Paul Pogba behind, United often gave the impression that they could do with some extra inspiration in the final third.
The Brazilian midfielder almost opened the scoring in the 16th minute, getting in front of Matteo Darmian to head a Toni Kroos corner against the bar from six yards.
The breakthrough came just past the midway point in the first half as Dani Carvajal was afforded the time to flight a ball over Victor Lindelof -- another United debutant -- for Casemiro to stretch and volley past David de Gea.
Mourinho sent on Marcus Rashford for Jesse Lingard at the start of the second half, yet it was at the other end that the chances kept coming.
De Gea repelled a Kroos piledriver but there was nothing he could do to stop Isco making it 2-0 in the 52nd minute.
Surrounded by red shirts just inside the area, Isco escaped their attentions by playing a one-two with Bale before coolly finishing past De Gea.
United had a mountain to climb and were not helped when Lukaku blazed over after Keylor Navas pushed a Pogba header into his path.
Lukaku did not make the same mistake twice, converting the rebound when a Nemanja Matic drive was not convincingly dealt with by Navas, but the goalkeeper redeemed himself with a vital late save to deny Rashford.
And Real, with Ronaldo on for the closing stages, held out.
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