They were heading for another draw, and a two-game points tally in Group C which would have equalled their worst start to a Champions League campaign of 12 years ago, when the 22-year-old Mexican received a ball played into his path by fellow substitute Federico Macheda, took one touch and – just nine minutes after arriving on the field – drove home the shot which takes United a big step closer to the knockout stage.
There was no stroke of luck about the finish, which gave United only their second win on Spanish soil in 18 years, though it is typical of them to strike so late.
The young man who answers to "Chicharito" (Little Pea) had already thrown himself at a low, dipping Nani cross and headed against Valencia's upright before striking a goal of infinitely more intent than the one which bounced in off his face in last month's Community Shield.
"The form of Berbatov has delayed his appearances and playing Wayne and Berbatov is the natural choice of the season," Sir Alex Ferguson said of the player last night. "He's not had a lot of football. He is young, he knows that. He is getting a lot of strength in the gym but he has work to do. He also has to work at that technique. But that goal... it was like he was shelling peas. He's a natural finisher with either foot. He has proved that tonight."
Macheda's vision in receiving Nani's pass and picking out the Mexican, rather than shooting, should not go unremarked, either. The Italian has that habit of making things happen in sharp time and, all told, the combination made yesterday's images of Wayne Rooney leaving Manchester's Bridgewater Hospital after a scan on his ankle recede a little further into the background.
For the first time since May, United have also avoided conceding a goal on their travels, and the sight of Rio Ferdinand's impeccable and possibly match- saving 72nd minute interception was another important staging post on a tricky evening and an erratic start to this season.
Ferguson's was a quiet kind of joy as he savoured Hernandez's strike, though the evening could – should – have taken a different course. But taking three points at a club whose current ascendancy in La Liga flatters them does not invalidate the view that the United manager will not find the going easy when the real work starts in February. At least a win against Bursaspor next month will all but take them to next spring's knockout stage.
The manager was justifiably content with Ferdinand's contribution. "For his first game in a long time in a real game, we must be very pleased with that," he said, also rejecting suggestions that his side were fortunate to get away with the win.
That said, and despite the fact that Edwin van der Sar had only one second-half save to make, it was an evening when his side's propensity for defensive errors did reveal itself once again. Rafael's eccentric positioning was one of the themes of the first half. Nani's need to fill in at right-back, as cover for the wandering Brazilian, deprived United of his own attacking presence, and he was helped out by Nemanja Vidic – whose personal start to the game was not helped by it taking fully the first two minutes to get his bootlaces tied.
The passing out of defence was as loose as those laces, for all the manager's assertions that his side had rectified the "very careless defending" that "has been our concern recently". It is on the kind of unforced errors like those United presented in the first half that games can turn. An abject ball from Nani, in that right-back's berth, to Michael Carrick, five yards in front of his own defence, saw him dispossessed and the in-form Roberto Soldado unleash a 20-yard shot narrowly over the bar.
Another careless ball out of defence by Ferdinand was propelled back into United's unoccupied right flank from where Alejandro Dominguez's looping cross deceived a culpable Van der Sar and landed on Soldado's head before he could anticipate it. The ball sailed on to the roof of the net.
Dimitar Berbatov ploughed the lone furrow as United put defensive resilience above ambition in a city – the last to fall to Franco in the civil war – which has a history of such qualities. It was he who created the early space, working the ball past two players and bending a 22-yard effort narrowly over only four minutes in. And he who, the other side of the interval, took down a 30-yard Darren Fletcher pass, breezed into the area and forced a good save from Cesar Sanchez. Berbatov continues to seem a player shaken out of last season's listlessness, for all that the complaints at his team-mates persist.
Valencia conceived one last push when Van der Sar turned away the substitute Manuel Fernandes's snapshot on 76 minutes. But Hernandez, not Fernandes, was the sub who was to count. "I have been settling in well in Manchester. I have been learning and working so hard because I want to do well here," the matchwinner reflected later.
"I have had pressure before. But I am very motivated in this team. I am confident to want the ball. I am enjoying it and it is great to be a player of Manchester United. I want that to continue for a long time." A confident, articulate individual, he sounds as much of a prospect as he looks.
Valencia (4-4-1-1): Cesar; Miguel, Navarro, Maduro, Mathieu; Pablo Hernandez, Albeda (Topal, 86), F Costa (M Fernandes, 74), Mata; Dominguez (Aduriz, 59); Soldado. Substitutes not used Moya, Saltor, Feghouli, R Costa Booked Aduriz
Manchester United (4-5-1): Van der Sar; Rafael (O'Shea, 90), Ferdinand, Vidic, Evra; Nani, Carrick, Fletcher, Anderson (Hernandez, 77), Park; Berbatov (Macheda, 85). Substitutes not used Kuszczak, Owen, Smalling, Gibson
Referee V Kassai (Hungary)
Man of the match Vidic
Attendance 52,689
Match rating 6/10.
Group C
Results so far: Bursaspor 0 Valencia 4, Manchester United 0 Rangers 0, Valencia 0 Manchester United 1, Rangers 1 Bursaspor 0.
Manchester United's remaining fixtures: 20 Oct Bursaspor (h); 2 Nov Bursaspor (a); 24 Nov Rangers (a); 7 Dec Valencia (h).
Man-for-man marking
Manchester United
Edwin Van der Sar
Lucky Soldado headed over from six yards after the keeper uncharacteristically missed a cross. Redeemed himself later on with a good save from a long-range drive. 6
Rafael da Silva
Put in a good shift in defence but occasionally showed signs of naivety. Struggled when the Spaniards upped the tempo. 6
Rio Ferdinand
Composed as ever, with him in the side United's defence looked so much more organised than in recent games. Some great interceptions. 8
Nemanja Vidic
Great positioning and made some crucial blocks but the movement of Soldado and Dominguez for Valencia caused him problems. 6
Patrice Evra
Not at his best, caught out of position at times and couldn't advance as much as he would have liked. Found it difficult against the tricky Pablo. 5
Park Ji-sung
Largely anonymous, tried to influence the game but had to track back for the majority of the match, helping Evra at left-back. 4
Michael Carrick
Endured a very busy night chasing the quick passing of Valencia. Lacked urgency when in possession but defended well. 6
Darren Fletcher
Comfortable with the ball and kept United ticking over alongside Carrick - did his best to break up play in the holding role. 7
Anderson
Drove the team forward in the first half in his best attacking display in a United shirt - but tired as the game wore on. Substituted. 6
Nani
A poor performance, wasteful at times with sloppy passes. Full of running down the right but could fire in only one dangerous cross. 5
Dimitar Berbatov
Cut a lonely figure up front but was let down by the service provided. Great touch to create toe-poked shot was his sole effort. Substituted. 5
Substitutes
J Hernandez (for Anderson 77): Marvellous run and finish for goal, look threatening as soon as he entered the field. 7
F Macheda (for Berbatov 85): Exploded out of the traps as soon as he came on - provided Hernandez with an assist with first touches. 7
O'Shea (for Rafael da Silva 92): Brought on to see out the match. n/a
James Orr
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