Striker Mamadou Niang headed a last-gasp goal from Franck Ribery's corner to give Marseille a 1-0 extra-time win at Le Mans.
"We knew we could make a difference on set pieces at the end and that's what we did by scoring from the last corner," Ribery said.
Five-times league champions Lyon, who have not won the Cup since 1973, were given a fright when Laon striker Vincent Koffmann scored on 20 minutes.
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Gerard Houllier's team equalised eight minutes later through Francois Clerc before a flick from Govou put Lyon ahead midway through the second half.
Striker Fred wrapped up the win with a spectacular volley five minutes from time.
"We made it hard on ourselves tonight. We should have scored at least two goals in the first half," said Houllier.
Lyon are still gunning for four trophies. Houllier's men have a 14-point lead in Ligue 1, play AS Roma in the Champions League first knockout round next month and meet Girondins Bordeaux in the League Cup final in March.
Lille spurned a two-goal lead before grabbing a 3-2 victory at Ligue 2 side Racing Strasbourg courtesy of a Yohan Cabaye goal 15 minutes from time.
Sochaux, who trailed fifth division Lyon-La-Duchere until the 77th minute, scrambled a 2-1 home win.
Romain Piteau levelled for the Ligue 1 high-flyers after Rachid Benayem had opened the scoring in the fourth minute.
Santos Alvaro then clinched victory in injury time. Bordeaux registered a 5-4 penalty shootout win over Ligue 2 Niort after a 3-3 draw following extra-time.
Ligue 1 bottom club Sedan ended the run of Calais by beating the amateurs 2-1.
Mansour Boutabout put Sedan in front on 26 minutes before fellow striker Marcus Mokake doubled their tally near the end.
Midfielder Samuel Marque grabbed a consolation goal in the 87th minute for fourth division Calais.
Ligue 2 Montpellier knocked out Nice 4-2 on penalties following a 1-1 stalemate.
Nantes advanced on Friday with a 3-1 win at Ligue 2 Amiens.
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