Qassim, 76, who last month underwent surgery, was convicted by a criminal court in May of illegal fundraising and money laundering.
Authorities had accused him of abusing his position as a cleric to "serve foreign interests and promote... sectarianism and violence."
The supreme court, whose rulings are final, also confirmed the same verdict for two of the cleric's aides, Sheikh Hussein Mahrus and Mirza al-Obaidli, the source said.
Qassim was being briefly hospitalised last month for blood pressure and diabetes-related treatment.
The cleric, revered by the Shiite community, was a leader of 2011 protests in the Sunni-ruled kingdom.
In another ruling, the supreme court on Monday upheld the death sentence against a Bahraini Shiite for murdering a policeman in a bomb attack in february 2013.
The court also upheld life terms for six other defendants and confirmed jail terms of six years and five years for two other men involved in the attack.
Bahrain has been shaken by unrest since security forces crushed Shiite-led protests demanding a constitutional monarchy and an elected prime minister.
The strategic Gulf kingdom is a key regional ally of the United States and serves as home for its Fifth Fleet.
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