Talks in Bonn between four Afghan factions agreed on an interim government which Mr Karzai would lead.
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For weeks diplomats have feared that Mr Karzai would annul the election.
Mr Karzai said Afghanistan would "definitely be able to provide for the security of the Afghan people".
Acknowledging his victory this week, Mr Karzai predicted that naming his ministers would be like opening Pandora's box.
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In her conversation with Mr Karzai, she promised that Isaf would do all it could do find out what had led to the killings in villages close to a US base.
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Regarding former members of the Taleban, Mr Karzai said those who had no criminal record would be freed.
Mr. Karzai was aware that his latest comments would cause outcry, but decided to go ahead anyway because he felt that complaints made to Western leaders behind closed doors were often ignored, Mr. Faizi said.
Mr. Karzai welcomed the spring transition time frame that would put his forces in the lead.
Mr Karzai said if Osama Bin Laden were caught he would be handed over to international justice.
Mr Karzai said he was "very happy" to hear that Afghan forces would take over responsibility for providing security by this spring.
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Rebooting Mr Karzai, assuming that he wins re-election and that it is possible, would be much better for his country than many more American brigades.
The presidents also agreed that the US would hand over custody of prisoners to the Afghan government, a step Mr Karzai said was critical for his country's sovereignty.
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The same day, Mr Karzai acknowledged that there had been intimidation but he expressed the view that about half of the delegates would be genuine representatives of the people, and that the process had gone "extraordinarily well" given the circumstances.
Mr Karzai has been reluctant to sign a long-term binding security agreement with the US amid fears it would undermine Afghan sovereignty.
Janan Mosazai, the Afghan foreign ministry spokesman, said Mr. Karzai was planning travel to Qatar at the invitation of the Gulf emirate, and he said the Taliban office would be a subject of discussion.
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