Alan Silva scored twice inside the opening 20 minutes, with the striker nodding Hugo Viana’s cross past David De Gea before finishing from close-range after great work by Eder on the wing.
Javier Hernández did manage to halve the deficit before half-time when the United forward’s header crept into the net despite the best efforts of Braga goalkeeper Beto.
United were on top in the second half, and Jonny Evans scrambled the ball over the Braga line from a corner to restore parity before Hernández completed the comeback with a superb header with 15 minutes remaining.
But despite an uncomfortable start to the game, Ferguson felt he was right to make changes to his line-up ahead of a tough run of fixtures which sees United play Chelsea and Arsenal in the coming weeks.
“We did the right thing [to rest Patrice Evra and Rio Ferdinand],” said Ferguson.
“It wasn’t Michael Carrick’s fault for the first goal. He did his job well and he was able to take the ball out of the back four and pass it terrifically.
“You have to look at the big picture. With Rio’s age, and we have a big a game on Sunday against Chelsea, and then Chelsea again on the Wednesday, followed by Arsenal on Saturday.
“We’ve a massive programme coming up now and it is important to utilise the squad that we have.”
Meanwhile, Ferguson heaped praise on Hernández and admitted the Mexico international’s performance has given him a selection headache, with Wayne Rooney, Robin van Persie and Danny Welbeck also vying for a starting spot.
“He’s improving all the time and such great enthusiasm for the game,” he added.
“He’s got me thinking. Hernandez, Van Persie, Rooney and Welbeck – I don’t know what to do with them.”
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