The announcement withheld the final election numbers, apparently as part of the political deal between Ghani and rival Abdullah Abdullah, a former foreign minister who claimed the process was rigged against him.
"The Independent Election Commission of Afghanistan declares Ashraf Ghani Ahmadzai as the president of Afghanistan," commission chief Ahmad Yousuf Nuristani said.
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"Although the audit was comprehensive ... (it) could not detect or throw out fraud completely," Nuristani said, without taking further questions.
Under the terms of the unity government deal signed on Sunday, Ghani will share power with a chief executive proposed by Abdullah. The two will share control over who leads key institutions such as the Afghan army and other executive decisions.
The new administration faces huge challenges in fighting an emboldened Taliban-led insurgency and paying its bills amid plummeting tax revenue.
It will also face significant difficulty in improving the lives of Afghans who face hard times as aid flows fall and as contracts with the NATO-led coalition dry up as most foreign troops leave by the end of the year.
The accord signed on Sunday was the finalisation of a broader power-sharing structure brokered by US Secretary of State John Kerry, who swiftly welcomed its signing.
"These two men have put the people of Afghanistan first, and they've ensured that the first peaceful democratic transition in the history of their country begins with national unity."
One of Ghani's first acts would be to sign a long-delayed bilateral security agreement with the United States, as he has previously declared support for the pact to allow a small force of foreign troops to remain in Afghanistan after 2014.
There is a risk that any instability could be exploited by neighbours, like Pakistan, whose past involvement in Afghan affairs have played a part in the conflicts that have dogged Afghanistan for decades.
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