The 26-year-old was expected to lead the African champions against their hosts at the Moses Mabhida Stadium in Durban, the site where he masterminded a 4-1 demolition of Mali in the Africa Cup of Nations last February.
Coach Stephen Keshi was quoted by KickOff: “Mikel has been withdrawn from the squad. He has a stomach bug.”
He joins the duo of Emmanuel Emenike and Kenneth Omeruo who had earlier withdrawn from the game.
It will be a big blow to the Super Eagles as they hoped to use this game to perfect tactics ahead of their final 2014 Fifa World Cup Group F qualifying game against Malawi next month.