Vioz took the decision on Friday, two days after the imam and three others were arrested in a police raid on An'Nour and houses in the surrounding area.
The raid followed a tip off about a sermon given by the imam in late October in which he “called for the murder of Muslims who refuse to participate in communal prayer”, Zurich's public prosecutor said a statement.
On Friday the prosecutor confirmed they will pursue criminal proceedings against the imam and a board member of the mosque for inciting crime and violence.
Two others arrested in the raid, including the mosque's former president, have been released after questioning.
In a statement announcing the mosque's suspension Vioz said the imam's words “contradict the commitment to Swiss rule of law and democracy that we ask of all our members”.
His actions have damaged the whole Muslim community in the canton of Zurich, it added.
In an interview with SonntagsZeitung on Sunday the president of Vioz, Mahmoud El Guindi, said the organization was “shocked” at the imam's sermon.
However El Guindi said he was against banning the An'Nour permanently.
“The suspension is meant to be a warning, but everyone deserves a second chance. We are a religious community and not a court of law. Our aim is not to punish people for illegal behaviour.”
He said Vioz was now investigating ways to better regulate the job of imam in order to prevent such a situation happening again.
The arrested imam probably didn't have the necessary qualifications, he added.