Sir Alex Ferguson's men must avoid defeat to FC Basle in Switzerland next month in order to book a place in the last 16.
However, they would almost certainly have to go through as runners-up as, though they are level on points with Benfica, they trail the Portuguese giants on head-to-head record.
United only have themselves to blame too after battling back from conceding an early goal to lead through goals from Dimitar Berbatov and Darren Fletcher, only to let Pablo Aimar snaffle another for the visitors, who are now through with only a home game against Group C whipping boys Otelul Galati to come.
To make matters worse, United's best player this evening, Michael Carrick, will miss the final game through suspension.
After five successive clean sheets, it came as a hammer blow for United to concede after only three minutes.
That the ball should be turned into the net by one of their own just made the pain more acute.
Benfica had already made a bright start when Nicolas Gaitan found himself enough space to whizz over a low cross that flicked off Patrice Evra.
Jones was well placed to clear, only to stick out a foot and turn the ball past stranded goalkeeper David De Gea.
Seven days after being likened to Franco Baresi by England manager Fabio Capello, this was the other side of the footballing coin for the 19-year-old, who looked somewhat shell-shocked as the visitors celebrated their good fortune.
With Wayne Rooney missing with the hip problem that kept him out of training and free-scoring Mexican Javier Hernandez on the bench, it was suddenly a major test of mettle for those Sir Alex Ferguson had called upon.
Initially it looked as though they would not rise to the challenge.
With Bruno Cesar, who went close with a 20-yard drive, and Gaitan pulling the strings, a second for Benfica looked a distinct possibility.
It was a Nani free-kick and Ashley Young's snap-shot that gave United the impetus to launch their fightback.
Leading the attack, Berbatov had not scored in Europe since his brace against Celtic in October 2008. If ever the £30.75million Bulgarian was going to prove his worth, this needed to be it.
And when Nani curled over an excellent cross on the half-hour, Berbatov finally delivered, touching his header into the far corner.
United should have been ahead a minute later when Berbatov sent Young through, only for the England man to drill a shot against Artur's legs.
Axel Witsel gave the hosts a scare moments later, although United were starting to gain control and it took an excellent tackle from Ezequiel Garay to deny Berbatov a second.
The momentum was maintained after the restart but for some reason, after jinking his way to within touching distance of the Benfica goal, Berbatov attempted to find Young with a cutback rather than squeeze out a shot himself and the chance was lost.
Fabio was denied by Artur after a forceful run from Jones before Evra delivered the brilliant cross that Fletcher met after making a perfectly-timed run.
Artur denied the Scot's first effort but from the rebound Fletcher had a tap-in.
Old Trafford breathed a collective sigh of relief.
But those who felt the hard work had been done were in for a nasty shock as De Gea's weak clearance allowed Cesar to charge into the United box.
Though his cross was blocked by Rio Ferdinand, Aimar gobbled up the rebound.
Young rightly argued he had not been offside before giving Berbatov the easiest of finishes. Unfortunately, Antonio Valencia had been and up went the flag.
Having dug his team out of one hole, Berbatov should have done it again 12 minutes from time when Fabio floated a cross into the box.
The striker beat the offside trap but, leaning back, sent his first-time volley over from 12 yards.
Hernandez's introduction for Valencia was a fairly obvious move after that but though United pressed, the elusive winner would not come.