The France international was introduced as a late substitute in the club's 0-0 draw away to Bastia on Saturday, but is now set to miss the home match with Saint-Etienne on Tuesday as well as the trip to Lorient on Saturday.
And his participation for the clash with Dortmund at Signal Iduna Park on October 1 is also in jeopardy with the striker set to miss up to 10 days of action.
"Verdict: toe tendon problem! 7 to 10 days," Gignac wrote on Twitter.
Gignac has started the season in impressive form, hitting three goals in six Ligue 1 fixtures.
Elie Baup's side sit fourth in the French top flight, just three points adrift of leaders Monaco.
They will be looking for their first Champions League points of the season against Jurgen Klopp's men, having lost their opening match 2-1 at home to Arsenal.
