The Blues were ahead 2-0 after the first leg and Lille responded quickly with the opening goal of the match after 38 minutes.
Turkish veteran Burak Yilmaz rifled past Edouard Mendy from the penalty spot after the referee pinged Jorginho for a handball after consultation with VAR.
But the reigning European champions responded three minutes into first-half stoppage time through Christian Pulisic.
Jorginho's clever pass found the pacy American behind the Lille defence and Pulisic finished off the neat play with a superb finish into the corner of the net from a tight angle.
The victory was completed with just over 15 minutes remaining thanks to a close-range goal from captain Cesar Azpilicueta.
Beset by distraction over sanctions of owner Roman Abramovich, the Blues brushed aside their woes to book their place in the final eight.
Thomas Tuchel's side must now turn their attention to Saturday's FA Cup quarter-final against Middlesbrough.
The west London club will be without any away support due to the UK government sanctions placed on Abramovich, which were prompted by Russia's invasion of Ukraine.
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