Approaching the 26th anniversary of Sir Alex Ferguson's appointment as Red Devils manager, the comeback was a suitably fitting way to preserve his side's 100% record and means, barring a complete collapse in their final three games, they will advance to next spring's knockout stage.
However, with two games against Chelsea and a home encounter with Arsenal to come before the return fixture in a fortnight, Ferguson must harbour serious concerns about United's fragile defence.
Incredibly, they have now fallen behind eight times in 12 games this season.
Tonight it took less than two minutes to surrender the initiative.
And they fell further behind before Hernandez struck, the Mexican capping a fine display by nodding home the winner from Tom Cleverley's cross 15 minutes from time.
It had been established in the five times United had gone behind since Michael Carrick had been eased out of central defence that he was not responsible for his side's repeated inability not to find themselves playing catch-up.
There had been evidence in the performances of Scott Wootton and Michael Keane in the Capital One Cup against Newcastle last month that there was an alternative should the need for an emergency central defender arise.
With Chris Smalling and Phil Jones still at least a fortnight away from full fitness and Rio Ferdinand rested to the bench, an assurance already received from Ferguson that it was solely to do with Sunday's visit to Chelsea and nothing to do with the weekend T-shirt spat, this was one such occasion.
Yet Ferguson again went for Carrick as Jonny Evans' partner, presumably on the basis Braga would not offer much of a physical threat.
Carrick lacks defensive nous though, and having shepherded Eder to the by-line, his failure to trap the Portugal international there was suicidal.
After turning sharply, Eder scampered towards the goal before cutting a cross back to provide Alan with an easy finish.
This would have been bad enough. The fact Braga were already in front raised serious concerns about United's ability to pull through.
Barely a minute had elapsed when Alan pulled to the far post and climbed above Alex Buttner, replacing Patrice Evra for the first European game of his entire career, and steered it past David de Gea.
It was the eighth time they had fallen behind this season, and the fourth occasion in the last five games, a quite shocking statistic that cannot continue if United are going to be serious challengers for silverware this term.
Predictably, a team skippered by Wayne Rooney and including Robin van Persie and a host of other stellar attacking talents, the hosts were a force at the other end.
A wise advantage by Serbian referee Milorad Mazic allowed Shinji Kagawa to profit from a foul on van Persie, crossing for Hernandez, who nodded home.
The pair would have combined to haul United level had an offside flag not been raised against Kagawa as he darted on to Van Persie's through ball before rolling another cross into Hernandez's path.
Ferguson noted that mistake, and a few others, in his half-time assessment of proceedings.
However, in hauling off Kagawa and introducing Nani at the break, the Scot was also signalling the diamond he feels could revolutionise United needs a bit more polishing before it is ready for public display.
The transformation was immediate as United sped down the flanks, pinning their opponents back.
As the crosses fizzed across Braga's goal, the visitors' defending became increasingly desperate.
When Evans took a fresh air swipe at van Persie's corner, the attempted clearance cannoned back off Elderson, allowing the Northern Ireland defender a second chance, which he duly prodded in.
It was Evans' second goal in three games, not a bad return considering he had only scored once in his previous 131 appearances for the Red Devils.
From that moment it was only a matter of time before United got their winner.
Tom Cleverley provided it with a superb, deep cross from the right touchline.
Hernandez, whose movement was akin to that he showed during his debut season, peeled away and headed home.