The electoral commissioner announced early on Monday that James Michel had come out ahead in the polls, taking 53.7% of the vote.
"I hereby declare Mr. James Alix Michel the elected president of the Republic of Seychelles," Hendrick Gappy, the electoral commissioner, said.
Michel beat back a strong challenge from Wavel Ramkalawan, an Anglican cleric who was making his fourth run for the presidency.
Ramkalawan took 45.7% of the vote, while Phillipe Boulle, an independent candidate, came in a distant third with 0.56%, Gappy said.
At the ceremony where the announcement was made, Michel described the victory "a great moment for me and a great moment for the people of the Seychelles," and called for unity following the tough electoral campaign.
"I will be the president of every Seychellois ... without discrimination," he said.
Ramkalawan told reporters: "It's a disappointment," but he said he would not challenge the results.
"There were no irregularities as such to challenge. It's the money they poured into the campaign. They bought it once again."
Ramkalawan said he would not
challenge the results
"The question is what will happen to our economy," he added.
Gappy announced the final returns after ballots were counted from the three-day exercise that concluded on Sunday on the three main islands.
Turnout among the island's 64,026 eligible voters was 88% with 30,119 ballots cast for Michel, 25,726 for Ramkalawn and 314 for Boulle, Gappy said.
Michel, who inherited the presidency from his political mentor two years ago, and was in his maiden quest to be elected, is to be inaugurated on Tuesday.
His win keeps intact the ruling Seychelles People's Progressive Front's 29-year grip on power on the far-flung chain of 115 islands despite opposition calls for radical change.