Only once had Manchester United won when two goals behind in the Champions League: the famous night in Turin when Roy Keane dragged them to a 3-2 victory over Juventus that led the way to the 1999 final.

On 75 minutes of an evening that again did nothing to ease the heart rates of the home congregation Javier Hernández was the man who changed this statistic, the Mexican's head connecting with a sweeping Tom Cleverley cross from the right to give United the lead. There were further scares. An 80th-minute corner from Alan, who scored both Braga's goals, careered around the area before the ball found a route into the hands of David de Gea. United ended proceedings as they began: living dangerously.

The first half had continued the thrills and spills in attack and the defensive mishaps that are the Manchester United movie this season. Yet even by their sluggish standards the start was dire.

The clock showed 80 seconds when they fell behind to an Alan header after Michael Carrick – later hoodwinked for the visiting captain's second – conceded a corner just after kick-off. This was defended but, when play continued and the ball broke to Hugo Viana, a swinging delivery from the left found the No30's head, who bested Alexander Büttner to give his side the lead.

This was the eighth time in 12 outings Sir Alex Ferguson's men have trailed during the campaign. Worse was to follow as the stunned Reds had their deficit doubled. This time Carrick, playing as an auxiliary central defender, was the patsy in a Cruyff turn executed by Eder down the left. The striker cruised towards De Gea's goal, then rolled the ball into Alan whose finish was expert.

For each of these goals the space United allowed when turned was the issue, a problem that continued throughout.

For the United faithful something like normal service was resumed after 25 minutes. Robin van Persie's tricky footwork moved him inside from the left. He was chopped down by Leandro Salino, the visiting right-back, but the referee, Milorad Mazic, allowed the advantage as possession moved to Shinji Kagawa. He floated a cross on to Hernández's head and, though Beto parried the ball, it followed him over the line.

Van Persie followed this with a neat chest-down and swivel-then-shot, though it went wide. There were further moments when United might have drawn level: Wayne Rooney's probing down the right with Rafael da Silva went unrewarded and Büttner's mazy run into the Braga area could have won a penalty as he fell.

But the jittery rearguard that has plagued United this season was again evident when a regulation clearing header from Da Silva was instead spooned behind to give Braga a corner.

With all six of the available points gathered, Sir Alex Ferguson had been content before the visit of the Portuguese. "The main aim tonight is to make sure we don't waste our advantage and we get the points which almost see us through," he told United Review. "A win would take us to nine points, just one from my target of 10 with three games left."

While 10 points does not always guarantee passage into the post-Christmas competition, as Manchester City learned last season, Rio Ferdinand, whose role in the proposed breakaway black players' union is yet to be clarified, was on the bench, with no place at all for Scott Wootton, who looked to have been in the running for a full Champions League debut alongside Jonny Evans.

Ferguson had lined his side up in a diamond shape for the second consecutive time of this group stage, with Rooney at the tip behind Van Persie and Hernández. This dynamic changed when Nani replaced Kagawa for the start of the second half, due to the knock to a knee he sustained during the opening period, and Rooney moved to the left.

With Nani on the right, Ferguson's men were now operating in a more orthodox 4-4-1-1, flat across midfield. The manager said: "I was confident that [the diamond] would be important but when you are 2-0 down it is easy for them to kill the game by playing it wide. We had to change that to stop the flow of their possession.

"In the second half Kagawa was injured anyway, it forced my hand to play Nani as a wide player and it made a difference to their possession."

After Da Silva won a free-kick on the right for which Elderson was booked, Van Persie stung Beto's fingers with a curving attempt from the angle. Rooney was next up, first pinging in a through-ball to Van Persie that was blocked, then offering the collectors' item of a cross with his left foot that did find the Dutchman, but again the danger was cleared.

Braga failed in this respect for Evans's equaliser. A Van Persie corner flicked off Carrick's back, Evans missed the ball but it rebounded to him off Alan and this time Evans scrambled it home.