The fixture was halted for more than 25 minutes after a group of home fans stormed the field at the Matmut Atlantique stadium.
Bordeaux's ultras stepped up their protests against the club's American-based ownership group King Street, whose motivations they have questioned, by entering the pitch after 10 minutes.
The delay continued after the supporters left the playing area and waited behind the goal, insisting on the return of their confiscated banners calling out the owners, president Longuepee and director of commercial strategy Antony Thiodet.
A group of fans brought back a banner to cheers and strung it up along one end of the ground. It read: "Against King Street and their two puppets Longuepee and Thiodet."
The match then resumed and Bordeaux, who sit third in Ligue 1 despite such off-field turbulence, moved into a 2-0 lead through a Josh Maja brace before half-time.
Longuepee said afterwards, according to L'Equipe: "This is a sad situation for the club. It's unacceptable and it is not at all the image that we want to give of football in Bordeaux and across France.
"It is all the more distressing taking into account the repeated calls for dialogue that we have proposed to the ultras.
"As you know, King Street is the majority shareholder in the club, committed to the Girondins [Bordeaux] for a long time.
"I would like to confirm to everyone that I will not resign. Bordeaux is an exciting club with ambitions and values that I will defend for a long time."
Reports in France have claimed King Street could seek to sell several of Bordeaux's players in the January transfer window, to recoup money invested, should it buy out fellow US-based shareholder GACP.