The French side capitalised on an error from Wayne Rooney shortly before the break to score the only goal at Stade de France, with Tottenham reject Milenko Acimovic providing the expert finish.
The Red Devils were nowhere near as bad as they were during the weekend loss at Middlesbrough that prompted Roy Keane's latest bout of straight talking, but this setback could prove to be far more costly.
Villarreal's 1-0 win at Benfica means all four clubs in Group D are still well-placed to qualify and United must find some form quickly if they are to avoid an embarrassing early exit from the competition.
With Paul Scholes suspended and a host of injury problems, Sir Alex Ferguson had few options available with his selection, but still managed to make several changes.
Wes Brown, Cristiano Ronaldo and Kieran Richardson all started after being named on the bench for the 4-1 defeat at Middlesbrough, with Phil Bardsley and Ji-Sung Park stepping down along with Scholes.
United produced a satisfactory first-half display, but the impressive response Ferguson expected after the drubbing at The Riverside failed to materialise.
The busy Ronaldo threatened to create chances for the visitors but a poor final ball let United down on several occasions. When they did create half-chances Richardson, Ronaldo and Rooney could not find the target.
At the other end of the field the Red Devils' backline looked shaky and John O'Shea and Rio Ferdinand both had to make well-timed tackles to prevent Matt Moussilou getting shots away.
Mathieu Debuchy headed wide from an Acimovic cross, before Geoffrey Dernis fired wide after dispossessing O'Shea, as the pressure on United's goal began to mount.
Seven minutes before the interval Lille broke the deadlock after a misplaced pass from Rooney to O'Shea.
The ball was picked up by Gregory Tafforeau, who surged down the left and sent over a low cross to Acimovic. The former Tottenham man cut between Brown and Mikael Silvestre before smashing a shot high into the goal.
The hosts almost doubled their lead early in the second half after Alan Smith brought down Acimovic just outside the box. Tafforeau's free-kick looked destined for the top corner, but Edwin van der Sar produced a spectacular save to push the ball over the crossbar and keep United in the match.
Ferguson's men were a whisker away from equalising just before the hour-mark, but Ronaldo's header from Rooney's corner bounced down from the crossbar and was cleared.
However, Lille continued to enjoy the better of the play and the increasingly rare chances fell to the hosts.
Moussilou wasted the best of them by heading over when unmarked before Dernis saw a long-range effort charged down, as the French side looked to make certain of the points.
United substitute Park made a hash of United's best chance of the evening with just six minutes to play, dragging a shot wide after a beautiful throughball from captain Ruud van Nistelrooy had sent him clear.