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.
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.
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.
