Argentinian playmaker Pablo Aimar's equalizer for Benfica on the hour mark ensured the Portuguese side a top-two finish in Group C and left United needing at least a draw in their final match, at Basel in a two weeks' time.
United goalkeeper David de Gea was at fault for Aimar's goal because of his poor clearance, and the hosts only had themselves to blame for falling behind in the third minute when England defender Phil Jones deflected a shot into his own net to gift Benfica a perfect start.
AP Photo
After a shaky first 20 minutes, United recovered and Dimitar Berbatov
equalized with a downward header from Nani's cross in the 30th, the
Bulgarian's first Champions League goal in three years.
A sustained barrage of pressure then culminated in Darren Fletcher putting United ahead for the first time in the 59th, tapping home a rebound after his initial shot was saved. But Aimar's leveler barely 60 seconds later was enough for Benfica to return home with qualification sealed.
The draw lifted Benfica above United to the top of the group by virtue of the head-to-head record between the teams. No matter what happens at home to Otelul Galati, the Portuguese side are through.
It's a different story for three-time winners United, who could be one of the group stages' biggest casualties if Basel can beat Alex Ferguson's men in Switzerland. The sides drew 3-3 at Old Trafford in September.
Since a 6-1 derby-day drubbing by arch-rivals Manchester City in the Premier League last month, United have had a heavier focus on defence, winning their last five games without conceding. That stingy run came to an abrupt end against Benfica - and it was one of the team's own players that did it.
Nicolas Gaitan's shot from an acute angle deflected off the leg of Patrice Evra toward Jones who, reacting late, could only turn the ball onto his own net from inside the six-yard box.
Rather than sting the hosts into action, it only served to rattle them. They were ponderous on the ball and misplaced many of their passes, frustrating the crowd and giving confidence to a quick-passing Benfica team.
United managed to recover their poise and soon the chances came. Chopped down after a mazy run, Portugal international Nani sent the free kick at goalkeeper Artur Moraes, who then saved a weak, left-footed effort by Young.
The breakthrough came when a free kick was shipped out to the left to Nani, who crossed for Berbatov to head down and into the corner.
United's sudden bout of sustained pressure continued into the second half and after Ashley Young and Fabio Da Silva wasted good chances, Fletcher put the team into the lead.
The Scotland midfielder met a cross from Patrice Evra with a shot that was well saved by Moraes, but Fletcher was on hand to tap home the rebound from close range.
Barely seen as an attacking threat for the previous 40 minutes, Benfica managed to reply almost immediately.
Again United were the architect of their own problems, with goalkeeper De Gea sending a sloppy clearance straight to Bruno Cesar, who collected the ball and drove into the area.
His fierce cross was only half-cleared by Rio Ferdinand, allowing Aimar to slam in from four yards out.
Berbatov squandered the best chance of either side to win the match, volleying over when all alone 10 yards out, although Rodrigo almost snatched the win for Benfica by flashing a low drive wide in the 89th.
In the other group match, FC Basel kept their Champions League hopes alive after holding out for a 3-2 victory over Otelul Galati after squandering a three-goal lead.
Basel raced into a 3-0 lead by half-time after Fabian Frei opened the scoring in the 10th minute, Alex Frei added the second and Marco Streller completed the scoring for the Swiss side in the 37th. Otelul's players showed more determination in the second half and their efforts paid off in the 75th minute when Gabriel Giurgiu fired home and Liviu Antal found the net just six minutes later.
But Basel held on for a point which leaves them in a position to qualify for the knock-out phase from their final Group C game - if they can beat Manchester United in Switzerland. Group leaders Benfica and United both have nine points, while Basel have eight, with Otelul on zero points.