State Department spokesman P.J. Crowley said Karzai used the 25-minute call to clarify his remarks.
"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," Crowley said, indicating that Clinton told Karzai that they should focus on common aims for stabilizing Afghanistan.
"They pledged to continue working together in a spirit of partnership," he said.
Earlier Friday, White House press secretary Robert Gibbs called Karzai's words "genuinely troubling," and Crowley said Karl Eikenberry, the U.S. ambassador in Kabul, met with the Afghan president Friday "to clarify what he meant by these remarks."
Karzai accused the United Nations and international community of trying to rig the presidential election in order to either deny him a second term or tarnish his victory. Afghanistan's election commission declared Karzai the winner of the Aug. 20 balloting, but a U.N.-supported independent complaints commission threw out nearly a third of his votes, forcing him into a runoff with challenge Abdullah Abdullah.
During his speech Thursday, Karzai acknowledged there had been "vast fraud" in the August vote, which returned him to office for a second five-year term. But he blamed the fraud on the U.N. and other foreign organizations.
"Suggestions that somehow the international community was responsible for any irregularities in the recent election is preposterous," Crowley said.