Results were due to be announced tomorrow from the vote in the Indian Ocean holiday paradise.
President Abdulla Yameen had voiced doubts over whether the elections commission could conduct the vote successfully after the chief and deputy were fired two weeks ago by the Supreme Court.
But private watchdog Transparency Maldives said the opening of the poll was "smooth, transparent and well-administered" and the government declared the vote had gone off peacefully.
A coalition partner of Yameen had petitioned the court Thursday seeking a delay of the polls, arguing the commission did not have its full complement of five members to hold a free and fair poll.
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The head of the Elections Commission and his deputy were dismissed March 9 for "disobeying" a court order to adjourn part of last year's presidential election eventually won in November by Yameen.
"The commission barely meets the quorum (of three) to hold an election of such importance," Yameen told a rally in the capital Male on Thursday.
More than two-thirds of the 240,000-strong electorate turned out to vote, officials said, citing preliminary estimates.
The dismissal of the two top election commission officials nearly two weeks ago has reignited the controversy over last year's presidential vote when the Supreme Court annulled the results of a first round won by Nasheed, and then cancelled two other polls at the last minute.
Yameen won the November 16 presidential run-off, five years after the island nation introduced multi-party democracy.