The France international suffered the injury during last night's surprise 1-0 defeat to Ligue 1 strugglers Troyes.
Gignac was taken to hospital for a scan, which revealed the extent of the injury.
A statement on the Marseille website read: "Andre-Pierre Gignac has suffered a fractured fifth metatarsal. He has been ruled out for six weeks, according to the medical staff of Marseille."
Marseille boss Elie Baup admitted after the match the injury blow was "bad news".
Gignac said on Twitter: "I am a fighter! I'll come back even stronger!"