The Red Devils rallied late on to come back from a goal down in Portugal to confirm their place in the knockout stages of the Champions League with four straight group stage wins.
Braga dominated the first hour of the game and was ahead early in the second when Alan converted a penalty for the home side. But United came out hungry after a power cut and turned the match around in the final 10 minutes thanks to goals from Robin van Persie and Wayne Rooney and a late strike from Javier Hernandez.
Chris Smalling made his first appearance of the season as United made six changes from the weekend win over Arsenal. Van Persie dropped to the bench, with Sir Alex opting for the front pairing of Danny Welbeck and Hernandez. Braga coach Jose Peseiro selected the same side which lost the return fixture at Old Trafford.
The home side had the first sight on goal in the fifth minute when Eder flashed a shot across David De Gea from a wide angle after Johnny Evans allowed the Braga forward through.
United managed to settle into the match following the early scare, but it was Braga which again came closest to scoring. Ruben Michel was invited to shoot by United's retreating defense but the midfielder could only curl his shot a yard wide of the top corner.
Michel continued to find space in United's half and Braga almost reaped the rewards when Eder's low diving header, from Michel's cross, hit the post with De Gea beaten.
The home side began the second period how it ended the first and was awarded a penalty only three minutes after the restart when Evans blocked off Custodio's run into the box. Alan stepped up and emphatically converted to the penalty to give Braga a deserved lead.
A power cut in the 57th minute delayed the game for 10 minutes, both sets of bemused players left the field of play while officials worked on the stadium's floodlights.
Rio Ferdinand replaced Evans when the game resumed, with Van Persie also coming on for Welbeck shortly after, as United pressed for an equalizer. Braga began to sit deep in its half after going ahead but continued to pose a threat on the break.
Sir Alex Ferguson's men began to show signs of life as the match edged into its final 10 minutes and brought the scores level in the 79th minute, thanks mainly to some poor goalkeeping from Beto. The Braga stopper misjudged a pass into Van Persie and needlessly came rushing off his line to allow the Dutchman a relatively easy finish from the edge of the box.
Moments later the turnaround was complete when United was awarded a penalty after Rooney was brought down in the area. Rooney took the spot kick himself and dispatched it with ease to secure United's perfect record in the competition this season.
Hernandez added a late third for the visiting side in injury time with a close range finish after a succession of errors in the Braga defense.
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