The Constitutional Court of the Republic of Indonesia on Thursday said former general Susilo Bambang Yudhoyono's sweeping victory was final.
It said Megawati had not submitted any objections by the Thursday deadline.
While Megawati has not made an explicit statement on her defeat in the historic 20 September vote, nor congratulated her former chief security minister, Susilo should now be free to declare victory.
He has held off assuming victory, waiting for any challenge to be dealt with, as financial markets and investors await details of his plans and cabinet choices following a grinding election season that began with a parliamentary poll in April.
Susilo is to be sworn in as the new
president on 20 October
"The deadline to lodge a complaint has passed without anything being lodged," constitutional court chief Jimly Asshiddiqie said.
The independent election commission said on Monday Susilo had won by 25 million votes. Both domestic and foreign monitors have said the vote was fair.
Asshiddiqie said the result was final and binding.
Susilo welcomed the court statement, saying he would concentrate on getting his government ready.
He said he would establish contact with Megawati to ensure a "peaceful and democratic change of leadership".
The former general is due to be sworn in as president on 20 October.
He has pledged to create jobs, clean up government, reverse drops in foreign investment and fight terrorism in the world's most populous Muslim country.