Gignac has been in sparkling form for Marseille so far this season, scoring five Ligue 1 goals in nine appearances.
Marseille manager Elie Baup confirmed that Gignac required hospital treatment following the match but does not yet know the extent of the problem.
He told the club's official website: "This is another negative point but we do not yet know how long he will be out for."
The 26-year-old French international forward spoke before going to hospital as he faced up to spell on the sidelines.
He said: "This is not good news. It's like that, it's part of life as a footballer but I have a lot of bad luck, and it's doubly so because we lost tonight."
A shock defeat to Troyes cost Marseille their place at the top of Ligue 1, allowing Paris Saint-Germain to leapfrog their bitter rivals on goal difference.