The centre-back was smacked in the face by Saint-Etienne goalkeeper Stephane Ruffier in the buildup to Jimmy Briand's equaliser. Just five minutes after Saint-Etienne had taken the lead, Ruffier rushed off his line to punch clear a cross from Maxime Poundje but caught Subotic and subsequently missed the ball. It then fell to Briand who was able to usher it over the line to level the score after 22 minutes.
Subotic fell unconscious for a while and had to be stretchered off with blood dripping down his head. The 29-year-old was then taken to hospital and is being kept in overnight for observation.
"Neven is going to stay here," Saint-Etienne coach Jean-Louis Gasset said. "The doctor has been advocating for a few days of observation."
The news will come as a big worry for Gasset, as Subotic has been a mainstay in Saint-Etienne's defence this season.
Less than 10 minutes after the former Borussia Dortmund player's injury, Saint-Etienne lost another defender as Mathieu Debuchy had to go off.
"I hope it will be a sprained ankle," Gasset said when asked about the extent of the right-back's injury.
Bordeaux went on to take the lead in the second half through a Francois Kamano penalty. Although Wahbi Khazri equalised for the visitors in the 67th minute, Pablo found a late winner for the home side.