The France international, 25, has not played for Les Gones since February 14 due to a groin strain and was expected to return to training this week.
But his prolonged absence means he will not face Saint-Etienne this Saturday and remains doubtful for much of the season run-in.
Former Milan and Bordeaux midfielder Gourcuff has only played seven Ligue 1 matches this season, scoring once.
Defender John Mensah, who returned injured from Ghana duty at the African Cup of Nations, is also absent but Lyon otherwise have a full first team to choose from.
Lyon lie seventh in a congested Ligue 1 table, four points off third-placed Lille, who they beat 2-1 last weekend.