Mardom-e Emrouz published the slogan next to a picture of Hollywood star George Clooney who had said it at the weekend's Golden Globes.
The words have come to symbolise the fight for freedom of expression after a January 7 deadly attack on the French satirical magazine Charlie Hebdo in Paris.
"The court in charge of cultural affairs and the media imposed the ban on the newspaper for publishing a headline and a picture which it deemed insulting," Mardom-e Emrouz director Ahmad Sattari told IRNA.
Its chief editor Mohammad Ghouchani also said the paper was banned "for having published something linked to Charlie Hebdo," according to the news website nasimonline.ir.
The attack on Charlie Hebdo's offices by two Islamist brothers killed 12 people.
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Clooney, who is also popular in Iran, joined tens of thousands of people around the world by paying tribute to victims.
"Je suis Charlie" (I am Charlie), Clooney told the audience at the Golden Globe on January 12 as he received an award for his film career.
Mardom-e Emrouz, which in Farsi means "Today's People", published on its front page a picture of Clooney and above it the headline: "Clooney: I am Charlie".
The paper triggered the ire of several conservative dailies who urged the prosecution to take action against it.
Iran denounced the Charlie Hebdo massacre on the day it occurred, saying the killings contradicted Islamic teaching.
But like many Muslim countries it also condemned the publication Wednesday by Charlie Hebdo of a new cartoon of the Prophet Mohammed holding a "Je suis Charlie" sign under the headline "All is forgiven".
The image has angered many Muslims as depictions of Mohammed are widely considered forbidden in Islam, and triggered protests Friday in Asia, Africa and the Middle East, some of which turned deadly.