United, who went on to win the tie 2-0 on aggregate, were fined 15,000 Swiss francs after their fans misbehaved in the same match, played on February 20 at Racing Lens's Bollaert stadium because Lille's own ground does not meet UEFA standards.
European football's ruling body said Lille were fined "for breaches of security provisions and lack of proper organisation, as well as for the improper conduct of the team after United's goal in the English side's 1-0 victory".
Earlier this month, UEFA threw out an appeal by Lille against the controversial late goal scored in the first leg by United's Ryan Giggs who fired in a free kick while the French team were still preparing their defensive wall.
Several Lille players seemed close to walking off the pitch in protest, although the club denied that was their intention.
There were crowd problems during the match including a crush caused by apparent overcrowding in the United end.
French officials said the problem was caused by several United supporters entering the stadium with forged tickets.
UEFA said on Thursday that United fans had set off fireworks and caused disturbances at the entrance to the stadium.
The teams can appeal against the fines within three days of receiving a written explanation.
"The club are waiting for a full explanation from UEFA but can already take into account the gap in sanctions regarding the two clubs", said Lille in a statement.
"The club judge this ruling extremely severe and disproportionate and will consider the option of lodging an appeal."
A spokesman for United said: "We have no comment to make at this stage as we have not yet received written explanation of the reasons for the fine."
More from rediff