Ligue 1 champions Lille dominated but were caught out by Matthieu Dossevi's opener in the 71st minute with Vincent Aboubakar adding the second seven minutes later. Nolan Roux scored a consolation goal two minutes from time.
Dossevi opened the scoring against the run of play when he volleyed home from a free kick and just when Lille looked set to equalise, Aboubakar made it two with a fierce shot at the end of a sharp counter-attack.
Roux reduced the arrears with a header and Lille were denied an equaliser three minutes into injury-time when Franck Beria's lob was cleared on his goal-line by defender Rafael.
Bafetimbi Gomis inspired Olympique Lyon to a 3-1 home win over Girondins Bordeaux in extra-time to book their place in the quarter-finals while Montpellier beat Ligue 2 side Chateauroux 2-0 away thanks to goals by Olivier Giroud and Younes Belhanda.
France striker Gomis fired home from close range six minutes into extra-time and started the attack that led to Jimmy Briand's goal, giving Lyon a deserved victory after Alexandre Lacazette had cancelled out Jussie's first-half opener for the visitors.
Bordeaux took the lead after 23 minutes when Brazilian forward Jussie ran into the area from the right to shoot past goalkeeper Hugo Lloris.
Seven-times French champions Lyon hit back 14 minutes later thanks to Lacazette, who scored into an empty goal after Cedric Carrasso had parried an Ederson header into the path of the striker.
Lyon centre-back Cris escaped a red card in the 85th minute after grabbing Yoann Gouffran by the shoulder as the forward was running towards goal.
The hosts, however, sealed victory when substitute Gomis latched on to Briand's fluffed volley to beat Carrasso, who had made a string of superb saves to keep his side in the match.
Gomis started a swift counter-attack that led to Lisandro Lopez setting up Briand for the French international to fire home in the 118th minute.
