It was the home side that took the lead after 49 minutes when Alan converted from the penalty spot. However, three late goals from Robin van Persie, Wayne Rooney and Javier Hernandez secured the points.
Here, Sports Mole dissects the 90 minutes of action between the two Group H rivals.
On target 4
On target 5
Was the result fair?
Yes. Braga were arguably the better side for an hour of the contest, but United dominated possession throughout the 90 minutes. There is no doubt that the stoppage in play helped the away side and you always felt that they would go onto win it after levelling 10 minutes from time.
6/10. Braga showed that they can compete at this level with a solid display this evening. They were always vulnerable in defence, but impressed with their ability to counter-attack. For large periods of the match they were the better side, but it was worrying the way that they collapsed after conceding an equaliser.
Manchester United's performance
6/10. It was hardly vintage from United, but how many times have we said that over the years? It simply does not matter how you play at this stage. It is about securing qualification as soon as possible. There is no doubt that Van Persie changed it for United, but they also defended well for large periods this evening.
Sports Mole's man of the match
Wayne Rooney: It was a close call between the England striker and Braga's Eder this evening. However, Rooney shades the accolade with his all-round performance from a deeper position. Also, he got back among the scoring.
Biggest gaffe of the match
This certainly has to go to the generator inside the stadium. We lost power for around 12 minutes in the second period due to a generator failing. It ultimately cost the home side.
Felix Brych had a fairly successful 90 minutes of action this evening. The referee allowed the play to flow in the correct areas, but was not afraid to distribute bookings when he felt necessary. He also rightly awarded two penalties.
Braga: The Portuguese outfit return to league action away to Sporting Lisbon on Sunday. Meanwhile, their next Champions League match is against Cluj on November 20.
Manchester United: United return to Premier League action away to Aston Villa on Saturday. Their next Champions League clash is away to Galatasaray on November 20.