In a statement, world football's governing body said it had suspended the PFF in accordance with the decision of the Bureau of the FIFA Council dated Tuesday.
The Pakistan soccer federation's "offices and its accounts remain in control of a court-appointed administrator", FIFA said.
The men's national team has not played a game since 2015, which has seen it slump to an all-time FIFA ranking of 200 and there is no professional football league.
They have also not been unable to send teams to major tournaments and has also failed to stage top-flight domestic competition.
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Pakistan football has not been in the best of health but this must be the ultimate jolt as FIFA has chose to suspend the country from worldwide competitions.
The suspension of Pakistan's membership rules out PFF and its associate clubs getting any benefits from any of FIFA or the Asian Football Confederation (AFC) facilities or development and training programmes, with the federation losing all of its membership rights.
The ban cuts off funding from Zurich, and bars national and club teams and officials from global games and meetings.
FIFA had warned they were considering suspending the PFF back in July if the National Federation was not handed back its headquarters and accounts amid an ongoing dispute with a rival body in the country, led by Arshad Lodhi. The chaos led to Pakistan Football teams missing out on numerous worldwide events during last two years.
It was then decided that the courts would take control of the PFF's offices and accounts until the crisis was resolved.
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The PFF will also be barred from all contact with other member associations for the duration of the ban.
They warned, however, that this would be "conditional on the strict implementation of an action plan and a regular reporting mechanism".
In July this year, FIFA gave a final ultimatum to authorities in Pakistan for handing over football affairs to elected-president PFF Faisal Saleh Hayat or face suspension.
"It's a big loss for us today as none of our players, coaches or referees now could travel overseas until we are suspended", Hayat said.
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