The message reads that the death of the prominent Shia cleric was saddening and grievous.
The hardworking researcher on Quranic sciences rendered lasting services to the Shia culture and nurtured outstanding students in Qom and Lebanon's seminaries, Rouhani said.
"I extend condolences to seminaries and noble people of Lebanon over the regretful loss of the thinker and researcher," he said.
Morteza-Ameli died at 74 on Saturday in a hospital in Beirut. He was an expert in Islam and Shia's history and was among scholars of Qom and Lebanon seminaries.
He left Qom for his homeland in 1993 after a 25-year stay to continue his research and teachings in southern Lebanon.
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