Common opposition candidate Ibrahim Mohamed Solih won last week's election with 58.4 percent of the ballot, or 134,705 votes, election commission chief Ahmed Shareef confirmed.
The commission had released what it called "interim results" on Monday, but the official outcome of the September 23 polls was pushed back to allow legal challenges over the vote's conduct.
"There were accusations... against all five members of the commission, and we received death threats via phone calls, Shareef said. "But we didn't consider the threats at all because the security forces are providing all five members with security."
Constitutionally the commission had till Sunday to announce the final result. He said there were "minor disparities" involving just one ballot paper out of 233,889 votes cast.
Outgoing president Yameen, who jailed or exiled most of his rivals during his turbulent five-year term, took just 96,502 votes or 41.6 percent, Shareef said.
Scores of Yameen's supporters had lodged complaints saying that they and other voters had not been allowed to cast their ballot. Some had also accused the commission of taking bribes.
Shareef said the commission would file defamation suits against their accusers.
An investigation was underway into the hacking of the commission's Twitter account two days before the vote, he added.
Nearly 90 percent of the electorate of 262,135 turned out to vote, according to the official results.
Private election monitors had warned that the electoral process was heavily weighted in favour of the incumbent, but the final results showed huge support for the opposition.
Solih was backed by four opposition parties, three of which had supported Yameen in a controversial 2013 run-off that saw the country's first democratically elected leader Mohamed Nasheed lose narrowly.
Solih is set to be sworn in on November 17 when Yameen's term comes to an end.
There had been intense speculation that Yameen could try to hold on to power despite losing to the 54-year-old political lightweight.
Yameen's hardline rule dented the Maldives' image as a honeymoon paradise and caused alarm to be raised abroad.
Suspecting a plot to impeach him, Yameen in February declared a state of emergency and arrested top judges as well as political opponents.
Shortly after his surprise defeat last week, Yameen freed five political prisoners. But scores of others -- including his estranged half brother Maumoon Abdul Gayoom, a former president -- remain incarcerated.
Despite the election upset, Yameen managed to retain leadership of his party at its first congress after the vote on Friday night.
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