The playmaker, who was replaced at halftime in the 1-0 home win over Maccabi Haifa in the Champions League on Wednesday, will be sidelined for 10 days with a thigh problem.
"He has a muscle strain behind his left thigh. He will take some time off," coach Laurent Blanc told reporters.
Gourcuff, who has scored four league goals this season, shrugged off a similar problem to play 79 minutes in Sunday's 1-0 victory over Stade Rennes.
"The pain is not in the same spot," said Blanc who is likely to use Brazilian Fernando as his replacement on Saturday.
St Etienne made a poor start to the season but have improved in recent weeks. They beat Nice 4-1 in the League Cup and claimed a 2-1 win at Monaco in Ligue 1, with new signing Gonzalo Bergessio on target three times.
A Bordeaux win would put pressure on second-placed Olympique Lyon who visit RC Lens in Saturday's late game.
Lyon, who trail Bordeaux by two points, crushed Debrecen 4-0 in the Champions League on Tuesday.
"We need to give our best at Lens because it will be a very tough game," said coach Claude Puel. "They will definitely be waiting for us."
Promoted Lens have failed to record a win in their last three league outings and are down in 13th spot.
Third-placed Olympique Marseille, beaten 3-0 by Real Madrid in the Champions League on Wednesday, host Monaco on Sunday.
Surprise packages Montpellier, in fourth spot, chase their fifth win of the season at bottom club Grenoble on Saturday.
Grenoble have lost all seven matches, scoring twice and conceding 14.
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