FIFA said the ban was handed down because of government interference in the running of the KFA.
Kuwait were also banned twice for government interference in 2007 and 2008 but the latest suspension could have ramifications for the February election that will decide the new president of world soccer's governing body.
The emirate is home to influential sports power broker Sheikh Ahmad Al-Fahad Al-Sabah.
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He is a former oil minister, honorary president of the KFA, a FIFA executive committee member and president of the Association of National Olympic Committees.
Sheikh Ahmad carries significant sway in the 47-member Asian Football Confederation.
Qatar beat hosts Saudi Arabia 2-1 to win last year's Gulf Cup.
(Corrects final para to show Qatar beat Saui Arabia)
(Writing by Yara Bayoumy; Editing by Tony Jimenez/Martyn Herman)
