Stephen Sizer, vicar of Christ Church, in Virginia Water, Surrey, used Facebook to highlight an article that said the official narrative of the 9/11 atrocity was "absurd".
The Diocese of Guildford launched an investigation after the Church of England vicar posted a link to an article entitled "9/11 Israel did it", and reportedly wrote: "It raises so many questions."
His comments appeared in the same week as the 70th anniversary of the liberation of Auschwitz.
Announcing the ban on Sizer, the new Bishop of Guildford Andrew Watson said the vicar's "anti-Zionist agenda has become a liability".
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He said Sizer also agreed to refrain from commenting on Middle East issues.
"Many who more moderately support the Palestinian cause and share his critique of a particular brand of Christian fundamentalism, themselves find Stephen's actions to be increasingly unhelpful and counter-productive, a fact he himself now recognises.
"In order for Stephen to remain in parish ministry, I have therefore asked for and received from him a solemn undertaking, in writing, that he is to refrain entirely from writing or speaking on any themes that relate, either directly or indirectly, to the current situation in the Middle East or to its historical backdrop," he said.
It is believed to be the first ban of its kind issued by the church, The Telegraph reported.
Nearly 3,000 people died in a series of four coordinated terrorist attacks by the Islamic terrorist group al-Qaeda on the United States in New York City and Washington, on September 11, 2001.