Mr Karzai accused foreign officials in Kabul on Thursday of seeking to weaken him and his government. The White House said his comments were "troubling".
On Friday, he told Secretary of State Hillary Clinton Afghans were grateful for the international community's help.
A state department spokesman described the conversation as "constructive".
"President Karzai reaffirmed his commitment to the partnership between our two countries and expressed his appreciation for the contributions and sacrifices of the international community," P J Crowley said.
Mrs Clinton told Mr Karzai that they should focus on common aims for stabilising Afghanistan, he added.
"They pledged to continue working together in a spirit of partnership."
'Misunderstood'
In his controversial speech, Mr Karzai admitted there had been fraud in the presidential and provincial council elections last August.
"No doubt that there was a very widespread fraud, very widespread," he told the Afghan Independent Election Commission (IEC).
"But Afghans did not do this fraud. The foreigners did this fraud," he added, singling out Peter Galbraith, the former deputy head of the UN mission, and the EU mission head Gen Phillippe Morillon for blame.
He accused them of involvement in a plot to install a puppet government. Both officials have denied the allegations.
On Friday, White House press secretary Robert Gibbs said Mr Karzai's words were "genuinely troubling", and that the US ambassador, Karl Eikenberry, had asked the president "to clarify what he meant".
During their telephone conversation, Mr Karzai told Mrs Clinton that "the Afghan people and Afghan government were grateful for the support and sacrifice of the international community for peace in Afghanistan and the world," the president's spokesman, Waheed Omer, said.
Mr Omer also insisted the speech had been misunderstood.
"There is a difference of opinion on certain issues between Afghanistan and its international partners, but the president wanted the international community to pay attention to the concerns of the Afghan people," he added.
The BBC's Kim Ghattas in Washington says the controversy has raised real concerns in Washington about how reliable a partner Mr Karzai is, with close to 90,000 US troops deployed in Afghanistan.
Senior US officials are also concerned that Mr Karzai has seemed unable to turn the page since the elections, hinting that Mrs Clinton had appealed to him to let go and move on, our correspondent says.
'Corruption'
Last Sunday, US President Barack Obama made his first visit to Afghanistan since taking office.
The trip was seen as an affirmation of US support for Mr Karzai, while at the same time allowing Mr Obama to stress the need for his Afghan counterpart to tackle corruption and other issues.
"The president was quite clear with President Karzai over the weekend of the necessary steps that have to be taken to improve governance and corruption in order to deal with the problems that we face there," Mr Gibbs said on Friday.
Mr Karzai is currently locked in a power struggle with parliament over his attempt to appoint all the monitors for Afghanistan's elections.
He was not declared the clear winner in the first round of the 2009 presidential vote, but emerged as victor after the challenger in the second round stood down, following several months of argument.
Mr Galbraith dismissed Mr Karzai's claims on Thursday, saying the suggestion that the UN would organise electoral fraud was "absurd".
He blamed the president and some electoral officials for the fraud.
BBC
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