Hojat-ol-Islam Safi, who was also the imam of one of Basra’s largest mosques, died in a hospital in the southern Iraqi city on Sunday morning.
His funeral was held in Basra a few hours later.
In his message, Ayatollah Sistani offered condolences to the family and friends of the cleric.
He said Hojat-ol-Islam Safi spent his life in promoting Islam and helping the faithful.
Ayatollah Sistani prayed to God to bestow mercy and remission on his soul and grant his bereaved family patience and fortitude.