Cisse notched his first goal of the game in the 64th minute after arriving as a substitute, and scored his second minutes later to guide his side into the next round of the competition.
Ligue 2 side Ajaccio produced one of the the biggest surprises of the round of fixtures as they defeated Montpellier 1-0 away from home.
Nicolas De Preville handed the home side the lead in the 26th minute, but Arles battled back through Mamadou Niang in the second half, while Teji Savagnier's late strike looked to have given them the win.
However, Gaaetan Courtet scored in the 90th minute to send the game into extra time. Courtet went from hero to zero as he missed a penalty in early in the first half of extra time, while Samuel Gigot was sent off for the visitors.
Arles managed to compose themselves despite being down to 10 men, and earned their place in the next round as Fawzi Ouaamar netted in the 102nd minute to fire them through.
Duhamel got the hosts back in front and Herve Bazile looked to have sealed the game in the 84th minute, but Kevin Diogo sent the match to extra time. Neither team looked like finding the net again until Duhamel netted with seconds left to break Clermont hearts.
Ismael Bangoura put the match beyond doubt in the 72nd minute, while Shechter added his second of the match in stoppage time.
Lorient booked their place in the next round of the tournament with a 2-1 victory over Evian at the Parc des Sports.
Daniel Wass handed the home side the lead in the seventh minute, but Valentin Lavigne levelled for Lorient minutes later. Jordan Ayew got the winner for the visitors in the 73rd minute with a strike from close range.
Results in full: Bastia 3-1 Auxerre, Reims 2-3 Arles, Montpellier 0-1 Ajaccio, Caen 4-3 Clermont, Nantes 4-0 Laval, Lens 0-2 Creteil, Evian 1-2 Lorient, Toulouse 1-3 Bordeaux