The Maldivian parliamentary speaker said on Thursday all 50 members of the Majlis voted for Mamun Abd al-Qayum, one of four candidates standing for the presidency.
The news comes amid unprecendent anti-government violence in the country.
With the main parliament vote cleared, Abd al-Qayum will have to seek public ratification of his election at a nationwide referendum by mid October, to start his new term from 11 November.
The Majlis, which consists of eight members appointed by Abd al-Qayum, used a secret ballot to choose who was to lead the atoll nation of 1192 coral islands scattered across the equator.
However, government sources in the Maldives said Abd al-Qayum, 64, was expected to sweep the election, as there was no serious challenger to the veteran leader who now has another five years in office.
The latest vote comes against a backdrop of unprecedented civil unrest in the capital island Male, where mobs at the weekend torched state buildings, following the killing of two prisoners by the country's National Security Service (NSS).
Riots in Male were caused by
'human rights abuses'
Abd al-Qayum has ordered the arrest of 11 NSS men following the prison riot, which left three dead and many more wounded.
Human rights group Amnesty International said the scale of civil protest in Male last weekend underlined people's anger at the blatant abuse of their rights.
"In response to the recent wave of protests, President Mamun Abd al Qayum must take urgent measures to stop the systematic repression of peaceful political activists, and radically reform the criminal justice system to safeguard people's human rights," said Amnesty.
Endemic torture and unfair trials, abuse of power by the security personnel, and lack of clear boundaries between the executive power and the judiciary are at the heart of the protests, it added.
"By repeatedly dismissing reports of human rights violations in the country, the Government of President al-Qayum has allowed perpetrators to continue to act with impunity.
"This has effectively perpetuated a cycle of repression eroding people's confidence in the state's institutions to protect their fundamental rights. It is high time that government authorities accept their own responsibility and failure to protect and promote human rights."