Counting of votes began soon after balloting ended at 4 pm local time. Elections Commission chief Fuwad Thowfeek said official results of the presidential run-off would be announced tomorrow.
Preliminary results, however, will be available before midnight, he said.
Parliament Speaker Abdulla Shahid informed MPs through a letter that a new president and vice president will be sworn in tomorrow at a special session of the House.
Long queues were seen outside most of Male's polling stations and many voters did not leave even after casting their ballot, media reports said.
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Facing heightened global pressure, President Mohammed Waheed, who took office when Nasheed resigned under duress in February 2012, stepped down and left the country before the run-off.
On Wednesday, the Maldives was expelled from the Commonwealth Ministerial Action Group, which is investigating the political chaos after repeated court interventions to prevent the presidential elections.
After two cancelled polls, foreign diplomats increasingly viewed delays as politically motivated and the European Union warned of "appropriate measures" if today's election failed.
Fuwad also confirmed that the poll panel had received fewer complaints today, compared to previous elections.