The closure was imposed by Iran's state press watchdog over the publication of an article that critics say undermined Islamic principles.
The controversial article was an opinion piece that questioned the Shi'ite belief that the Prophet Muhammad had appointed his son-in-law, Imam Ali, as his successor.
Culture Minister Ali Jannati claimed the article distorted the history of Islam and created religious divisions.
"Unfortunately, 'Bahar' has committed several [press] violations in the past year-and-a-half. It has received written warnings, but the daily has not paid attention," Jannati was quoted as saying by the semiofficial Mehr news agency.
The hard-line daily "Kayhan" reacted to the piece by accusing reformists of attacking the rule of religious figures.
Alaedin Zohurian, the head of the Supervisory Press Board, was quoted by state media as saying that the newspaper’s case has been referred to the Judiciary.
The official action was taken despite an apology from "Bahar," which issued a statement on October 26 that said the article was not meant to be published. It also said it had voluntarily decided to suspend publication for two weeks to "ease tensions."
The banning of "Bahar" comes amid what appears to be a slight opening of the country's media atmosphere.
Rohani, who campaigned on a platform of relative moderation, has spoken in favor of freedom of press and speech.
Several Iranian journalists interviewed by RFE/RL in recent weeks have said that they feel less pressure from authorities and are less inclined to practice self-censorship. Some have even begun testing the boundaries by reporting and writing on sensitive topics.
A number of publications that have been banned in recent years are reportedly being reinstated, and there have also been attempts to revive the Association of Iran's Journalists.
The move against "Bahar" is, for some, a discouraging sign and a reminder of threats against press freedom in the Islamic republic, which has been branded by rights groups as one of the biggest jailers of journalists in the Middle East.
UN Special Rapporteur on Human Rights in Iran Ahmed Shaheed said in a report issued last week that at least 40 journalists -- as well as 29 bloggers and online journalists -- are currently serving prison sentences in the country.
A journalist who works at "Bahar" told RFE/RL: "The actions of the new government suggest that there is no place for journalism that raises criticism. More journalists are becoming jobless."
The journalist said it was the eighth time a publication he worked for had been either banned or suspended. Over the years, dozens of reformist and independent publications have been banned by Iranian authorities.
The popular news website Asr-e Iran criticized the ban against "Bahar" and other publications.
It wrote, "The time for a collective punishment has come to an end. End the execution of media." Asr-i Iran also called on authorities to reconsider their press policies, writing, "The closure of a media outlet is the same thing as firing its employees. It creates problem for their families, who haven't had any role in the mistake."