Frank Lampard's side were in complete control for the most part and set up the victory they required with first-half goals from Tammy Abraham and Cesar Azpilicueta.
Chelsea's nerves were frayed when former striker Loic Remy pulled one back for Lille late on but they were able to close out victory to reach the last 16 after finishing a tough group in second place behind Valencia but ahead of last season's semi-finalists Ajax.
"We had to fight and recover after losing against Valencia at home in our first game. But now we are in the last 16 the focus has to switch back to the Premier League until the competition starts again next year."
Abraham added:"I'm very excited to be in the next round. We came into the match needing to win and thankfully we did. Now I can't wait for the next round.
"It's just about getting into the box. Luckily for me I was in the right place at the right time."
On conceding late in the game, he said: "For us it is about sticking with it. We started so well, sometimes we just need to kill off games and to do that we need to score more goals."