Robert Gibbs, the White House press secretary, said on Monday that "President Karzai has been declared the winner of the Afghan election... So obviously he's the legitimate leader of the country".
Gibbs said that Obama's decision whether to add to US troop numbers in Afghanistan would come in the forthcoming weeks, as planned.
"This decision was not dependent upon when a leader was determined. We've never said that," he said.
"Now begin the hard conversations," he added.
Spencer Ackerman, a senior reporter for the Washington Independent, told Al Jazeera that the outcome of the Afghan election process had placed the US in a difficult position.
"They really have the worst of both worlds here - there is no way, procedurally, to remove the taint of fraud in the first round of elections, and yet they are stuck with the result.
"The Obama administration [is likely] to focus on governance below the national level, to see if they can get a more legitimate or accepted method of governance out in the provinces beyond Kabul. But there is really no way that they can ignore the Karzai government."
Afghanistan's election panel announced incumbent Karzai's victory in the presidential election on Monday after a runoff planned for November 7 was cancelled.
Karzai's second term in office adds pressure on the US in considering Afghan strategy
Azizullah Ludin, chairman of the Independent Election Commission (IEC), declared Karzai victor at a news conference in Kabul, despite telling Al Jazeera earlier that cancelling the runoff would be unconstitutional.
"Under the law, there is no alternative but to have these elections," Ludin had said.
Zekria Barakzai, the IEC's deputy chief electoral officer, contradicted Ludin's initial statement, telling Al Jazeera later: "Today's decision by the IEC was according to the provision of the constitution which requires at least two candidates for the second round."
The discovery of widespread fraud in the first round resulted in Karzai losing his more than 50 per cent advantage forcing him into a second round.
The validity of the electoral process and the independence of the IEC have both been called into question.
Abdullah cited the government's refusal to accept his demands for changes to the IEC for his decision to leave Karzai as the sole candidate in the runoff.
The cancellation of the runoff followed a meeting on Monday involving Ban Ki-moon, the UN secretary-general, Karzai and Abdullah.
Earlier in the day, Karzai had made a plea in an interview with a local radio station calling on Abdullah to reconsider his decision and participate in the runoff, Al Jazeera's James Bays in Kabul reported.
|Karzai had urged Abdullah, left, to reconsider his decision to quit the runoff [EPA]
Bays said that holding the election with one candidate would have posed a "vast organisational headache" and "security headache" even though voters would have been turning out for just one candidate.
The first round of Afghanistan's elections on August 20 was so badly affected by ballot-box stuffing and distorted tallies that more than one million votes were thrown out.
Abdullah had demanded electoral reforms that included the sacking of Ludin and suspension of four ministers who campaigned for the incumbent president.
He told supporters on Sunday a "transparent election is not possible" and that the Afghan government has been illegitimate since May.
"I'll not take part in the election," Abdullah had said, adding that he had "not taken this decision easily".
In an interview with Al Jazeera shortly after the announcement, he said the decision was made after "a lot of consultations".
"It was the right decision, and I did it in the best interests of this country," Abdullah said.