The national election board said on Tuesday Ahmed Abdullah Mohamed Sambi, nicknamed "Ayatollah" by his supporters, garnered 58% of votes, in a poll intended to draw a line under a history of inter-island strife and coups since independence from France in 1975.
Long-time politician Ibrahim Halidi, who was backed by the outgoing president, Azali Assoumani, won 28.08% of the vote, while deputy parliament speaker Mohamed Djaanfari garnered only 13.72%, the election board said.
Ali Abdallah, the secretary of state for elections, had announced the victory of Sambi late on Monday.
Sambi, 48, a cleric and successful businessman educated in Iran, Saudi Arabia and Sudan, was the favourite due to his strong showing in an April primary on Anjouan island that winnowed the field from 13 to three candidates.
Considered a moderate, he has spoken in support of an Islamic government on the impoverished, overwhelmingly Muslim archipelago.