Auxerre edged the all-Ligue 1 tie against St Etienne, while Nancy join them in the fourth round.
Sammy Traore's extra-time strike gave Auxerre victory over St Etienne after the clash had ended goalless after 90 minutes.
Nancy eased past Ligue 2 side Boulogne 3-0, Gaston Curbelo sending them on their way to victory just before the break.
Sebastien Puygrenier doubled Nancy's lead in the 68th minute before Benjamin Psaume scored an own goal with two minutes left.
Nancy 3 Boulogne 0
Brest 1 Montpellier 2
Niort 3 Le Havre 2
Auxerre 1 St Etienne 2