Cristiano Ronaldo watched most of the end-to-end action from the bench, while his teammates outclassed United Cup on a hot night.
Casemiro hit the bar with a header and fired a shot over the top before scoring in the 24th minute. The Brazilian slid in for a left-foot finish, served up by Dani Carvajal.
Isco extended the lead for Zinedine Zidane’s European champions with a cool shot in the 52nd, after Gareth Bale helped him run through United’s defence.
Making amends for an earlier miss, United’s new striker Romelu Lukaku made it 2-1 in the 62nd, beating Keylor Navas after the goalkeeper had blocked a powerful shot from Nemanja Matic.
"Key to winning this game was two things we do well," Zidane said. "We hold and control well, and we finish our chances at the right moment."
He added: "The second half was not great, but the first half was spectacular. We have talented players who want to win every challenge. That how they want to grow as players."
The players needed two cooling breaks to cope with temperatures of 32C (90 F) that led to three fans being hospitalized.
The Super Cup pitches the previous season’s Champions League winners against the Europa League holders.
It was Zidane’s second consecutive Super Cup title – while United coach Jose Mourinho failed in his third attempt to add the trophy to his collection.
United matched Madrid for pace but lacked the finishing to turn the match around. Henrikh Mkhitaryan, who regularly burst forward, and substitute Marcus Rashford provided much of United’s threat.
Both Rashford and Paul Pogba missed glaring second-half chances, failing to score with Navas at their mercy.
The game was watched by former United coaching great Alex Ferguson. Ronaldo came on after the 80th minute and had little chance to make an impact as Madrid closed down their opponents.
Moments before the final whistle, a shirtless fan ran onto the pitch and was wrestled to the ground by stewards.
More than 2,500 officers policed the game in the tiny Balkan country. Four people were arrested, accused of selling black market tickets. Authorities reported no major public disturbances after the match ended.
Following the award ceremony, Mourinho handed his medal to a young fan and later joked that he saw no point in holding onto it.
"Sometimes when I win I don’t keep the medal, so imagine when I lose," he said. "For me, the medal would go to some place in my house and for that kid, it’s the moon."