When Jonathan David stroked a first-time finish through the legs of the unfortunate Gregor Kobel in the fifth minute, the French hosts gained the lead.
After a 1-1 draw in the away leg in Germany, it gave Lille a 2-1 aggregate lead.
Dortmund responded in the second half after coming near on multiple occasions, and they tied the score in the 54th minute when captain Emre Can scored a penalty after Thomas Meunier had pushed Serhou Guirassy in the area.
In the 65th minute, Maximilian Beier made apologies by blasting into the roof of the goal after Guirassy’s pass had gone just wide.