"In protest at the mass killing of the people of Bahrain by its government, Mehdi Aghajafari, the ambassador of the Islamic Republic of Iran, has been recalled from Bahrain," the statement read.
The tit-for-tat move came a day after Manama recalled its ambassador to Iran in protest at Tehran's "blatant interference" in the Gulf kingdom's internal affairs.
Iranian officials have severely criticised the violent crackdown in Bahrain, and the dispatch of Saudi and Emirati troops there to help confront pro-democracy protests.
Defence Minister Ahmad Vahidi told the official IRNA news agency Bahrain had committed a "strategic and political" blunder that would cost its "legitimacy," when it asked Gulf troops to help quell pro-democracy protests.
Bahraini police firing shotguns and tear gas crushed the camp in Manama of a month-old pro-democracy protest on Wednesday in an operation that left five people dead.