Lille keeper Tony Sylva was still lining his wall up when Ryan Giggs calmly stroked his free-kick into the top corner seven minutes from time to secure a 1-0 win.
The home players raced to Dutch referee Eric Braamhaar, clearly unable to comprehend how the official had allowed the goal to stand.
But Braamhaar was not for turning and triggered a quite stunning reaction from the home bench, with the signal clearly going out for the Lille players to head to the sideline and end the game.
Thankfully, sanity prevailed and the contest continued, allowing United to claim a victory in a game which, until those bizarre last few minutes seemed set to be remembered for the chilling security scare inside the visitors end where fans seemed to get crushed in front of a 10 foot barrier.
Mercifully, no-one was injured in the incident, although that was hardly due to the actions of the riot police, who fired tear gas into the enclosure.
The diversion to the visiting section of the ground behind Edwin van der Sar's goal as the security problem was unfolding took attention away from what was an awful game.
It was fully 42 minutes before either side mustered a shot on goal, the half chance created by the willingness of Wayne Rooney and Henrik Larsson to press the ball deep inside the Lille area.
Ronaldo was on to the opportunity in an instant but, with red-shirted defenders flying on to the scene, the Portugal winger could do no more than fire straight at Tony Sylva, who blocked the shot with his body.
Lille responded almost immediately as Mathieu Bodmer drilled a 20-yard shot wide after Nicolas Fauvergue had extravagantly chested the ball into his path.
Aside from those opportunities, there was virtually nothing to enthuse either set of supporters, with the busiest man on the pitch being referee Braamhaar, who booked four men.
Thankfully for United, none of them was Paul Scholes, who knew a caution would rule him out of the return leg.
Certainly the aggressiveness Ferguson highlighted in Lille's play from those two dreadfully disappointing encounters last year had not disappeared, with Ronaldo getting increasingly agitated at the robust manner in which his skills were being blunted.
Thankfully for all concerned, the action improved markedly after the break and Ronaldo should have been the first to benefit from a much more open affair when he sped past Gregory Tafforeau into the Lille area.
Ronaldo may have 15 Premiership goals to his credit this term but he is yet to score for United in 23 appearances in this competition and was unable to break his duck as he blasted against Sylva.
The rebound was by no means a tap-in but Rooney should have done much better than fire meekly over.
Lille quickly responded and Mathieu Bodmer soon found himself in half a yard of space too close to the United goal for comfort. Thankfully for the visitors, Edwin van der Sar was alive to the danger and flicked the resulting shot wide with his foot.
The hosts thought they had scored after 62 minutes when Peter Odemwingie rose above Vidic to glance home Ludovic Obraniak's cross.
However, Braamhaar came to United's rescue, ruling out the goal for a push on Vidic by the Lille forward.
Both sides continued to press forward. Louis Saha, introduced for the ineffective Ronaldo, stabbed Patrice Evra's cross straight at Sylva before Odemwingie curled a shot just wide of the far post.
Another United break ended with Henrik Larsson chipping narrowly over after Sylva had failed to hold Wayne Rooney's low cross which had been intended for Ryan Giggs.
Johan Audel was unable to turn Matthieu Chalme's near-post cross goalwards as he slid in ahead of Nemanja Vidic, then Giggs' attempted lob never looked like dropping in after Scholes had lifted a pass beyond the Lille defence.
The Welshman soon found his range though and in doing so unleashed a storm of controversy that left Braamhaar to face a barrage of abuse as he left the field.
