Earlier, Western mass media reported that the article, titled "Europe and Us," in the small-circulation newspaper Senet, accused Islam of standing in the way of humanity's development and said that the Prophet Mohammed was responsible for all the misunderstandings concerning the Muslim religion.
Prosecutors said the article's author, Rafiq Tagi, will also be jailed for two months.
The Azerbaijani Prosecutor General's Office earlier said that the chief editor, Samir Sedagetoglu, and Tagi will be charged with inciting ethnic, racial or religious hatred through the mass media.
Sedagetoglu said he and his employees have received a number of phoned death threats, even after a televised apology to all who were offended by the article. He said he has asked prosecutors for protection.
The case is not the first when Muslims have protested against perceived insults to their religion. Last fall, a Danish newspaper published cartoons depicting the Prophet Mohammed. Muslims protested the publication, saying it was offensive to their religion, which bans any depiction of the Prophet.
The cartoons were later reprinted in other European publications, which cited press freedom.
The scandal reached Russia, home to 20 million Muslims, when a newspaper in the Central Russian city of Volgograd was closed down in February for publishing a cartoon featuring the Prophet Mohammed, Jesus, Buddha and Moses.
A popular media Web site, Gazeta.ru, received a warning from Russia's national media and cultural watchdog.
Protests across the Islamic world saw Danish products boycotted and Danish diplomatic missions torched.
