Hossein al-Najati was responsible for collecting and redistributing religious donations on behalf of Sistani.
Manama accuses Najati of not being transparent and said he did not have the official approval of the regime, Press TV reported.
"As none of the required procedures had been taken, it was decided to deport Najati in accordance with the laws and regulations in Bahrain," the Interior Ministry said .
Shiite opposition parties have condemned the cleric's expulsion, saying the move violates international laws and human rights.
His deportation is said to further stoke tensions in the Persian Gulf Island.
Najati had been among the 31 opposition figures deprived of their Bahraini nationality by the regime in 2012.