After a campaign dominated by economics issues and opposition calls for an end to his party's 29-year grip on power, the incumbent took 53.7 percent of the vote to win a five-year term as leader of the Indian Ocean archipelago.
Mr Michel bested activist priest Wavel Ramkalawan, who took 45.7 percent in his best showing yet in four runs for the presidency, and easily outdistanced independent candidate Phillipe Boulle who garnered just 0.56 percent.
"It's a great moment for me and a great moment for the people of the Seychelles," Mr Michel said after the official results were announced from the three-day exercise.
"I will be the president of every Seychellois ... without discrimination," he said, calling for unity after a tough campaign that had raised fears of political unrest on the 115-island chain of some 85,000 people.
Opposition concedes defeat
Mr Ramkalawan, an Anglican cleric, accepted defeat and said he would not challenge the results, but accused Michel's ruling Seychelles People's Progressive Front (SPPF) of electoral misconduct, including vote-buying.
"It's a disappointment," he said, urging Mr Michel to follow through on his promises to govern fairly in blunt remarks.
"This election was not held on a level playing field."
"I just hope that he is sincere when he says he wants to work for every Seychellois," Mr Ramkalawan said. "Unfortunately, we have heard these nice sounding words before but they have not amounted to much."
Initial reports from international observers indicated the polls, which opened on outlying islands on Friday and Saturday before moving to the three main ones on Sunday, had been largely free and fair.
Mr Ramkalawan's Seychelles National Party (SNP) had held high hopes for the election believing they had tapped into growing disenchantment with the government, which critics say is riddled with corruption and cronyism.
Despite spirited calls for radical change and a controversial proposal to devalue the national currency to deal with a severe foreign reserve shortage, voters handed Mr Michel a slim victory of less than 4,500 ballots.