Karzai reportedly did not apologise during the phone call with Clinton, but according to a US official quoted by the AFP news agency "he expressed surprise that his comments had created what he called a stir".
The call came after Karl Eikenberry, the US ambassador to Afghanistan, visited Karzai seeking "to clarify what he meant by these remarks".
Waheed Omer, Karzai's spokesman, said that parts of the Afghan president's speech had been misunderstood.
"Obviously 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 and the Afghan government."
Karzai's international reputation took a battering when a UN-backed fraud watchdog threw out one-third of the votes cast for him last August.
But on Thursday, Karzai said neither he nor election officials appointed by him were responsible for the violations.
"There was fraud in presidential and provincial council elections - no doubt that there was a very widespread fraud, very widespread," he said.
"But Afghans did not do this fraud. The foreigners did this fraud."
He said foreigners also wanted to interfere with parliamentary elections scheduled for September this year.
"Foreigners will make excuses, they do not want us to have a parliamentary election," Karzai said.
"They want parliament to be weakened and battered, and for me to be an ineffective president, and for parliament to be ineffective."
Karzai is battling the Afghan parliament and the UN over fraud-protection measures for the parliamentary vote due in September.
The lower house of parliament on Wednesday threw out a presidential decree revoking the power of the UN to appoint the majority of members of the election fraud watchdog.
The UN has called for reforms to Afghanistan's election commission to prevent fraud, before it will agree to free up donor funds needed to pay for the September 18 vote.
Thursday's accusation had prompted an angry reaction from Afghan rivals and international diplomats, who said that Karzai was responsible for all the vote rigging.
Abdullah Abdullah, who pulled out of a second-round run-off with Karzai saying it was impossible for it to be free and fair, told Al Jazeera: "He succeeded inadmitting the fraud, but he didn't in blinding the people and distorting the reality.
Peter Galbraith, the former UN head of mission in Afghanistan, said that the remarks were "extraordinary" and that it was an interesting admission on Karzai's part that "he now thinks there was a vast fraud, which is of course what I said right from election day".
"It was President Karzai and the people he appointed to Afghanistan's election commission that committed the fraud that got over one million phoney votes for Karzai.
Galbraith, who was dismissed by the UN after criticising it for not doing enough to combat voter fraud, was singled out by Karzai as having organised the fraud and fed details to the international media in an attempt to blacken his name.