The directive came in response to a case filed by a political party demanding that the results of the first round on September 7 be annulled because of alleged discrepancies.
"We order the Elections Commission and other relevant state institutions to delay the second round of the presidential election scheduled for 28 September 2013 until the Supreme Court issues a verdict in this case," read the ruling from the Supreme Court.
The court decision sparked protests by his supporters during which police pepper-sprayed Nasheed and beat and detained two MPs from his Maldivian Democratic Party (MDP), a member of Nasheed's security staff told AFP, asking not to be named.
Nasheed, 46, won the first round comfortably with 45.45 percent of the vote and faced a run-off contest on Saturday against Abdullah Yameen, the half-brother of the islands' former autocrat Maumoon Abdul Gayoom.
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Nasheed resigned in February last year after a mutiny by police that he branded a coup, allegedly orchestrated by Gayoom, who ruled the honeymoon islands for three decades.
The Election Commission confirmed to AFP that it had stopped all preparations for Saturday's vote in the country, home to about 350,000 Muslims spread across more than 1,000 coral-fringed islands.
Nasheed's opponents had raised concerns about the commission and the electoral rolls before and after the first vote, leading to fears of a contested result that would lead to more uncertainty.