Afghanistan has a new president

Ashraf Ghani gestures as he addresses a news conference in Kabul on July 5.

• NEW: "The new government will face serious challenges," U.N. chief says


• State Dept.: Audit found "significant" fraud, but results legitimate


• Abdullah and Ghani agreed to national unity government earlier in day


• The deal comes after months of dispute between the two candidates

Kabul, Afghanistan (CNN) -- Ashraf Ghani Ahmadzai is the new President of Afghanistan, and his rival, Abdullah Abdullah, is CEO, Afghanistan Independent Elections Commission chairman Ahmad Yousuf Nooristani announced in a news conference in Kabul on Sunday.

Nooristani didn't disclose the percentage of their votes from the June runoff election. He also didn't take any questions from journalists.

Ghani and Abdullah signed a power-sharing agreement earlier Sunday after months of infighting over allegations of voting fraud and manipulation.

The U.S. State Department congratulated both candidates, as well as the people of Afghanistan, "who courageously went to the polls to vote on April 5 and again on June 14, defying Taliban threats to exercise their right to vote and to take their part in advancing democracy in Afghanistan," according to a statement.

Afghanistan 'on the right track'

The statement also recognized incumbent President Hamid Karzai for 13 years of "strong leadership."

The lengthy dispute between Ghani and Abdullah had put off the selection of a successor to Karzai and raised fears of increased instability in the fragile, war-torn country.

But the two rivals embraced after signing a deal for a national unity government in a televised ceremony in the capital, Kabul, on Sunday.

Under the agreement, Ghani will create by decree the position of chief executive officer for the runner-up. The CEO role will have prime ministerial functions until the constitution can be amended to create a permanent position of prime minister.

The deal also calls for the two candidates' teams to share senior government positions equally between them.

The political impasse in Afghanistan this year had come as the Taliban continued to mount deadly attacks on high-profile targets and fought fiercely for control of important areas.

As the U.S.-led war effort against the militants winds down, most NATO troops are due to withdraw from Afghanistan by the end of this year.

'Three months of squabbling'

The presidential election was held on April 5 and was followed by a runoff vote in June after the first round proved inconclusive. The election was aimed at bringing about Afghanistan's first democratic transfer of power, but the accusations of fraud and manipulation put that goal in peril.

In July, Abdullah and Ghani had come to an agreement, brokered by U.S. Secretary of State John Kerry, to accept the result of a nationwide audit and form a unity government.

But earlier this month, the two candidates showed signs of backing away from that deal.

Kerry described the signing of the deal Sunday as "a moment of extraordinary statesmanship," saying Ghani and Abdullah had "put the people of Afghanistan first."

U.N. Secretary-General Ban Ki-moon said the deal "paves the way for a stable and more prosperous future for the country."

"The new government will face serious challenges, and I urge the President-elect, the Chief Executive Officer, Dr. Abdullah Abdullah, and all political actors in Afghanistan to quickly form the government of national unity," Ban said in a statement.

The State Department statement said that while the audit was able to "identify fraud that was significant in both scope and sophistication," the audit process was unable to resolve all grievances. Nonetheless, the election results are legitimate, and the State Department will support the administration's efforts to make electoral reform a chief priority, the statement said.

The White House and the U.N. Secretary-General's Special Representative for Afghanistan, Jan Kubis, both expressed support for the new government.

But questions remain about how effective the new arrangement is likely to be.

"It took three months of squabbling and political infighting to get to this point," Yaroslav Trofimov, the Afghanistan and Pakistan editor of The Wall Street Journal, told CNN. "It's anybody guess how well they will manage to actually govern together, considering all the bad blood."

CNN's Masoud Popalzai reported from Kabul, and Jethro Mullen reported and wrote from Hong Kong. CNN's Eliott C. McLaughlin, Nana Karikari-apau, Christabelle Fombu and Tom Dunlavey contributed to this report.