Chelsea started the game better of the two sides and after asking all the questions they found the opener through Tammy Abraham. He tapped home a pass from Brazilian international Willian in the 20th-minute mark.
Cesar Azpilicueta outjumped the french club defenders inside the six-yard box to head home Emerson's corner as the Blues increased the tally.
Former Chelsea striker Loic Remy reduced the deficit for Lille in the second half. The Blues held onto the slim margin as the referee called for the end of proceedings at Stamford Bridge.
Elsewhere, Chelsea's Group H opponent Ajax were been crashed out of the competition after losing at 1-0 home to Valencia who topped the group after their win.
Over at San Siro, Inter Milan also bowed out of the Champions League after losing the final group game 2-1 to Barcelona.
Napoli 4-0 Genk
Salzburg 0-2 Liverpool
Ajax 0-1 Valencia
Benfica 3-0 Zenit
Chelsea 2-1 Lille
Dortmund 2-1 Slavia Prague
Inter 1-2 Barcelona
Lyon 2-2 RB Leipzig