Toure had finished the season with Manchester City last month without any ill effects but the federation said he had suffered an injury without giving more details.
Interim coach Ibrahima Kamara is also without Yaya's brother Kolo Toure, who retired from the international game after Ivorian success in the Nations Cup in Equatorial Guinea at the start of the year.
The Ivorian squad for the trip to Libreville includes Wilfried Bony, Gervinho and Salomon Kalou, who were all part of the Nations Cup winning side in February.
Sunday’s match in Libreville forms part of the African Nations Cup qualifying campaign although the result will not count as Gabon are hosts of the 2017 finals.
(Reporting by Mark Gleeson in Cape Town, editing by Justin Palmer; mark.gleeson@thomsonreuters.com; +27828257807; Reuters Messaging: mark.gleeson.thomsonreuters.com@reuters.net)
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