Afghan President Karzai Agrees to Runoff Election

Afghan President Hamid Karzai agreed today to a runoff election against his top challenger after a U.N.-backed audit found that he had failed to win more than 50 percent of votes in the fraud-plagued election.

Flanked by Sen. John Kerry, D-Mass., chairman of the Senate Foreign Relations Committee, and U.N. Special Representative Kai Eide, a visibly tired Karzai defused what the U.S. feared would be a crisis if he rejected the Electoral Complaints Commission report. Instead, Karzai declared the runoff legal and constitutional.

Video of President Obama talking about the election in Afghanistan.Play

Earlier this week, the ECC threw out more than 1.3 milllion votes cast on Aug. 20 as fraudulent. Most of those votes -- 1 milliion of them, according to Democracy International -- had been marked for Karzai and made up one-third of Karzai's total. The reduction brought Karzai's tally to 48.3 percent, Democracy International claimed. Those figures were confirmed to ABC News by election officials.

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The IEC has questioned the U.N. commission's findings, claiming that Karzai's tally was 49.67 percent – a number that still triggers a runoff but is higher than the count by the ECC.

VIDEO: The Afghan president caves to international pressure for a runoff election.Play

"Although the IEC has some reservations," the group said in a statement, "considering the time constraints, the imminent arrival of winter and existence of the problems in the country...the second round of the elections will be held."

Karzai will now face off against his top challenger, Abdullah Abdullah, in a Nov. 7 runoff.

Karzai told the war-battered nation in a televised address that "1.3 million votes were decided to be suspicious. Most of which – around 1 million – were from southern Afghanistan. I call upon our nation to change this into a nation to strengthen our resolve and participate in the new round of elections."

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Karzai's decision ends days of speculation that he or the IEC might reject the commission's findings and refuse a runoff, creating an impasse in the Afghan government and further complicating the Obama administration's Afghan strategy.

President Obama, whose administration has been pressuring Karzai to agree to a runoff, praised the Afghan president.

"President Karzai's constructive actions established an important precedent for Afghanistan's new democracy," Obama said. "The Afghan Constitution and laws are strengthened by President Karzai's decision, which is in the best interests of the Afghan people. "

Obama called Karzai personally to express his appreciation for accepting certification of the Aug. 20 voting results. He also made calls to Abdullah and U.S. ambassador to Afghanistan Karl Eikenberry.

Kerry said of the news, "A moment of great uncertainly has been transformed into a moment of great opportunity." He praised Karzai for what he called "genuine leadership."

"His agreement to move the process forward with respect to the runoff will allow the national leadership to rule with legitimacy," Kerry said. "Dr. Abdullah Abdullah has made the same decision. Both have made their commitment to building a lasting democracy."

Kerry and French Foreign Minister Bernad Koucher have been in Kabul urging the Afghans to resolve the standoff quickly. Kerry met with Karzai five times in five days.

Focus Turns to Second Vote

With the Afghan runoff set for a little more than two weeks from today, preparations for the nationwide vote are now in full swing.

"Afghan plans are in place to enable a second round of voting," U.S. Secretary of State Hillary Clinton said today, "and we pledge our support to the election authorities to help them achieve a conclusion to the elections process." Clinton has said previously that ballots have been printed and that Afghan and coalition forces have begun devising security strategies.

Among the challenges facing election officials is impending winter weather in northern Afghanistan that could make it difficult for voters to reach the polls. The U.S. Embassy in Kabul has been poring over weather maps for months and is convinced that only small parts of the north will be too snowy for people to vote in the first week of November.

Officials say it's also imperative that the root causes of voter fraud and abuse that plagued the first vote be resolved before the runoff. Peter Galbraith, the former U.S. deputy to the U.N. senior representative in Afghanistan, told ABC News that unless officials make drastic changes to the election process, the second vote will be a "complete disaster."

Galbraith has been critical of the United Nations for its handling of last summer's election and was recently fired from his post after feuding with U.N. officials whom he alleges were complicit in the fraud.

He says many of the factors that caused problems on Aug. 20 -- ghost polling stations, corrupt election staff and a partisan election commission -- are still present.

State Department spokesman Ian Kelly said Tuesday the Administration is confident the risk of fraud has been reduced and that the second vote will be fair.

"They put in place some very specific technical trip wires and mechanisms to be able to catch fraud, and the system worked," Kelly told reporters.

Kelly refused to say whether Secretary Clinton warned Karzai about fraud in a runoff election during any of their numerous conversations in recent days.

The outcome of the runoff election will have enormous implications for the Obama administration's ongoing Afghanistan strategy review, which officials have said hinges on having an effective and credible Afghan partner.

Obama has said a pervasive sense of illegitimacy in Afghanistan among the Afghan people for their government would make the U.S. task "much more difficult."

Afghan Situation: 'Crisis of Legitimacy'

Today, Obama praised the work of the ECC and IEC as a step toward enhanced political legitimacy. "The United States has been interested above all in the strength and independence of those institutions, and the need for them to fulfill their mandate on behalf of all Afghans," he said.

An Afghan government seen as illegitimate also complicates the recommendation by Gen. Stanley McChrystal to send tens of thousands of more troops into the country to more closely partner in a counter-insurgency and nation-building strategy. Obama has delayed a decision on McChrystal's request for additional troops.

Sen. John McCain, R-Ariz., praised the upcoming runoff, but said it is unrealistic to expect Afghan governance to improve significantly without improved security.

"It is essential to implement the properly-resourced counterinsurgency strategy that Gen. Stanley McChrystal and our senior commanders have called for," he said, "and that is why I continue to urge President Obama to provide our military and civilian leaders in Afghanistan with the resources they need as quickly as possible."

ABC News' Martha Raddatz, Kirit Radia and Sunlen Miller contributed to this report.