The 26-year-old, who has been battling with injuries since he joined Lyon in 2010, tore the internal lateral ligament of his knee after six minutes when he collided with Troyes midfielder Benjamin Nivet on Saturday.
"He will be out for six weeks to three months, depending on how he recovers from his injury," Lyon said.
Gourcuff, who has 29 caps for France, played only 13 league matches with Lyon last season and failed to make the squad for France's Euro 2012 campaign.
He had looked on track to recover the form which helped him become the key player in Girondins Bordeaux's conquest of the French title in 2009.
He was named man of the match at the Champions Trophy when Lyon beat Montpellier on penalties last month to claim the season's first title. Gourcuff then scored the only goal in Lyon's opening Ligue 1 victory at Stade Rennes a week ago.
Lyon, who will not feature in the Champions League this term for the first time since 2000 after last season's fourth-place finish, top the Ligue 1 table with six points from two games - ahead of three other teams on goal difference.