United, who won the shootout 2-1, took the lead just before halftime when Anthony Martial slalomed into the box past three defenders to set up Jesse Lingard from close range.
Both sides made a raft of changes at the break, which upset the rhythm of the game. The sweltering conditions were also a factor as players struggled to get the tempo back up, while the 65,109 fans eagerly awaited the next goal.
It came in the 69th minute after Victor Lindelof took Real's Theo Hernandez down in the box and Brazilian Casemiro scored from the penalty spot.
Casemiro would get another chance from the spot in the shootout but hit the crossbar with Real's fifth kick to leave United the winners.
The first four penalty takers all missed, prompting incredulous laughter from a crowd denied much of a game in the second half. Henrikh Mkhitaryan and Daley Blind found the net for United while Luis Miguel Quezada was the only Real Madrid shooter to score.
Jose Mourinho was pleased to get the win but emphasized it was nothing more than a training exercise. His only real concern from the game was midfielder Ander Herrera limping off just minutes after coming on as a substitute in the second half.
"I also always say to the players, no risk in friendlies," said Mourinho. "If you feel something, or if you feel something is coming, get out, because the result is not important."
Real Madrid coach Zinedine Zidane was encouraged by what he saw from his team in their first pre-season match.
"It was our first game and we did quite well against a team that has had four or five games under their belts. I think that's a positive," Zidane told reporters.
"We hope we continue to find our form fast and that's what we're working on."
The two sides are to meet again in the UEFA Super Cup on Aug. 8 in Macedonia, which will be a much more competitive affair.
European champions Madrid next play Manchester City while United face Barcelona on Wednesday.
(Editing by Peter Rutherford)
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