The emergency committee of the world governing body said the blanket ban would come into to place with "immediate effect" which means no Nigerian team, including club sides, can play in regional, continental or international competitions.
In the wake of Nigeria's exit to France at the last 16 of the World Cup, the high court of the West African country ruled that its federation would cease to run the national team, handing over the role to a government civil servant.
This is in breach of a FIFA rules that obliges member associations to manage their own affairs "independently and with no influence from third parties," it said in a statement.
Stephen Keshi, the coach of the African champions, resigned the day after the 2-0 defeat, after leading the Super Eagles out of the group stages of the World Cup for the first time since 1998.
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