Mr Boni took 74.51 percent of votes based on 97.20 percent of all ballots, Benin’s independent election commission said, compared to 25.49 percent garnered by his rival, political veteran Adrien Houngbedji.
They were the final candidates following a first-round vote on March 5 to replace the country’s longtime leader Mathieu Kerekou.
“Democracy is the sole winner,” said election agency head Sylvain Nouwatin, expressing gratitude to voters who “acted with calm and serenity.”
Participation in Sudnay’s final round was 67 percent, slightly less than for the first round when more than 70 percent of the country’s four million eligible voters turned out.
Mr Boni had been widely predicted to win the run-off and replace Mr Kerekou, who has ruled for 30 of the last 34 years but was constitutionally banned from taking part in the poll, having passed the 70 years age limit.
A former head of the West African Development Bank, Mr Boni entertained a horde of visitors at his residence in Cotonou.
He told them he intended to build a government of “young, clean, just and new men”.
He said he intended to stress “the fight against corruption and create wealth to eradicate poverty” while developing relations and trade with Benin’s powerful and much larger neighbour, oil-rich Nigeria.
Boni said he intended engaging in “good governorship and transparency”, starting with declaring his assets should he be confirmed as president.
Born in 1952 into a Muslim family in the north of the country, Mr Boni was raised by an uncle and later converted to Christianity. He received a doctorate in economics in France, but three of his five children currently study in the United States.
International observers from the European Union, the Economic Community of West African States (ECOWAS) and the United States have praised the polls and electoral agency’s work under sometimes difficult circumstances.